Variant report

Variant	rs12640984
Chromosome Location	chr4:1338834-1338835
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:1338367-1339162	MCF-7	breast:	n/a	n/a
2	POLR2A	chr4:1338340-1339406	HepG2	liver:	n/a	n/a
3	CTCF	chr4:1338760-1338910	MCF-7	breast:	n/a	n/a
4	POLR2A	chr4:1338285-1339130	SK-N-MC	brain:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:1295898..1297425-chr4:1338423..1340843,2	MCF-7	breast:
2	chr4:1338699..1344021-chr4:1351274..1357737,7	MCF-7	breast:
3	chr4:1336595..1339547-chr4:1340996..1343146,3	MCF-7	breast:
4	chr4:1236808..1249320-chr4:1336333..1343819,66	MCF-7	breast:
5	chr4:1338673..1343611-chr4:1344125..1350325,16	MCF-7	breast:
6	chr4:1282437..1287650-chr4:1338224..1344043,13	MCF-7	breast:
7	chr4:1292718..1295595-chr4:1336898..1340190,3	MCF-7	breast:
8	chr4:1003354..1005738-chr4:1337401..1338947,2	MCF-7	breast:
9	chr4:1323033..1328941-chr4:1337055..1342245,8	MCF-7	breast:
10	chr4:1337039..1339011-chr4:1871068..1874025,2	MCF-7	breast:
11	chr4:1336558..1338149-chr4:1338227..1340765,3	MCF-7	breast:
12	chr4:1280840..1286312-chr4:1338111..1343712,9	K562	blood:
13	chr4:1235141..1249133-chr4:1336906..1347308,118	MCF-7	breast:
14	chr4:1280977..1287340-chr4:1335495..1344055,33	MCF-7	breast:
15	chr4:1313002..1315500-chr4:1338426..1340938,2	MCF-7	breast:
16	chr4:1188846..1191354-chr4:1337880..1340557,2	MCF-7	breast:
17	chr4:984860..987749-chr4:1337412..1341360,3	MCF-7	breast:
18	chr4:1239502..1245378-chr4:1336996..1344860,21	K562	blood:
19	chr4:1289122..1291329-chr4:1338444..1340407,2	MCF-7	breast:

No data

Variant related genes	Relation type
UVSSA	TF binding region
ENSG00000159674	Chromatin interaction
ENSG00000163945	Chromatin interaction
ENSG00000127415	Chromatin interaction
ENSG00000109685	Chromatin interaction
ENSG00000253399	Chromatin interaction
ENSG00000196810	Chromatin interaction
ENSG00000159692	Chromatin interaction
ENSG00000145217	Chromatin interaction
ENSG00000127418	Chromatin interaction
ENSG00000090316	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10024996	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1128427	0.85[EUR][1000 genomes]
rs12647145	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13117476	0.87[EUR][1000 genomes]
rs13118159	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13147602	0.83[EUR][1000 genomes]
rs1882105	0.80[EUR][1000 genomes]
rs2276903	0.87[EUR][1000 genomes]
rs2293630	0.86[EUR][1000 genomes]
rs2878608	0.86[EUR][1000 genomes]
rs34947293	0.87[EUR][1000 genomes]
rs3796613	0.81[EUR][1000 genomes]
rs3903127	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4974553	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4974604	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4974605	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4974608	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6843025	0.86[EUR][1000 genomes]
rs71614967	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7655119	0.81[EUR][1000 genomes]
rs7656122	0.81[EUR][1000 genomes]
rs7664474	0.86[EUR][1000 genomes]
rs7679860	0.83[EUR][1000 genomes]
rs7690727	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
5	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
6	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
8	nsv997971	chr4:1191256-1518521	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
9	nsv461155	chr4:1203265-1352685	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
10	nsv593281	chr4:1203265-1352685	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
11	nsv593298	chr4:1244267-1342521	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
12	nsv878338	chr4:1277826-1358449	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv878339	chr4:1277826-1363886	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv878340	chr4:1277826-1386570	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
15	nsv878341	chr4:1277826-1391400	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
16	nsv1002635	chr4:1282603-1402761	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
17	nsv878342	chr4:1291337-1363886	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
18	nsv878343	chr4:1291337-1391400	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
19	nsv878344	chr4:1291337-1414684	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
20	nsv878345	chr4:1291337-1563920	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
21	nsv461157	chr4:1300077-1352685	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
22	nsv593301	chr4:1300077-1352685	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
23	nsv878346	chr4:1300077-1363886	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
24	nsv878347	chr4:1300077-1866358	Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
25	nsv878348	chr4:1305269-1386570	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
26	esv1794294	chr4:1307119-1817474	Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
27	nsv878349	chr4:1318132-1363886	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
28	nsv878350	chr4:1320023-1500753	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
29	nsv932661	chr4:1324751-1364014	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
30	nsv878351	chr4:1329847-1414684	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
31	nsv878352	chr4:1334721-1363886	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
32	nsv1008785	chr4:1335089-1518521	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
33	nsv536988	chr4:1335089-1518521	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
34	nsv593302	chr4:1338618-1414684	ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12640984	UVSSA	cis	Thyroid	GTEx
rs12640984	CTBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1303600-1339400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:1317800-1339600	Weak transcription	Right Atrium	heart
3	chr4:1333400-1339400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:1333800-1339200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr4:1333800-1339400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:1333800-1339400	Weak transcription	K562	blood
7	chr4:1334000-1339400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr4:1334000-1339400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:1334000-1339400	Weak transcription	Hela-S3	cervix
10	chr4:1334400-1339600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:1334600-1339400	Weak transcription	HSMMtube	muscle
12	chr4:1335000-1339400	Weak transcription	Aorta	Aorta
13	chr4:1335200-1339000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:1335200-1339400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:1335200-1339400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr4:1335200-1339400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:1335200-1339400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr4:1335200-1339600	Weak transcription	Small Intestine	intestine
19	chr4:1335400-1339000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr4:1335400-1339000	Weak transcription	Fetal Brain Female	brain
21	chr4:1335400-1339000	Weak transcription	Fetal Intestine Small	intestine
22	chr4:1335400-1339200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr4:1335400-1339400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr4:1335400-1339400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:1335400-1339400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:1335400-1339400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:1335400-1339400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:1335400-1339400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr4:1335400-1339400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:1335400-1339400	Weak transcription	A549	lung
31	chr4:1335400-1339400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr4:1335400-1339600	Weak transcription	Ovary	ovary
33	chr4:1335400-1339600	Weak transcription	Psoas Muscle	Psoas
34	chr4:1335400-1339600	Weak transcription	Right Ventricle	heart
35	chr4:1335600-1339000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:1335600-1339000	Weak transcription	Primary T cells from cord blood	blood
37	chr4:1335600-1339000	Weak transcription	Liver	Liver
38	chr4:1335600-1339000	Weak transcription	Brain Angular Gyrus	brain
39	chr4:1335600-1339000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr4:1335600-1339000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:1335600-1339000	Weak transcription	Thymus	Thymus
42	chr4:1335600-1339400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr4:1335600-1339400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:1335600-1339400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr4:1335600-1339400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:1335600-1339400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr4:1335600-1339400	Weak transcription	Brain Hippocampus Middle	brain
48	chr4:1335600-1339400	Weak transcription	Brain Substantia Nigra	brain
49	chr4:1335600-1339400	Weak transcription	Colon Smooth Muscle	Colon
50	chr4:1335600-1339400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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