Variant report

Variant	rs4974549
Chromosome Location	chr4:1314948-1314949
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:1281929..1283740-chr4:1313199..1316127,2	MCF-7	breast:
2	chr4:1313002..1315500-chr4:1338426..1340938,2	MCF-7	breast:
3	chr4:1314077..1316689-chr4:1338914..1341716,2	MCF-7	breast:
4	chr4:1282487..1285160-chr4:1313904..1316772,2	MCF-7	breast:
5	chr4:1310884..1316010-chr4:1322677..1327905,6	MCF-7	breast:
6	chr4:1313294..1315156-chr4:1320127..1321902,2	MCF-7	breast:
7	chr4:1241359..1243168-chr4:1314910..1317673,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163945	Chromatin interaction
ENSG00000090316	Chromatin interaction
ENSG00000196810	Chromatin interaction
ENSG00000159692	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11247992	0.99[ASN][1000 genomes]
rs11727297	0.88[ASN][1000 genomes]
rs13129712	0.92[ASN][1000 genomes]
rs13147602	0.88[ASN][1000 genomes]
rs1680083	0.88[ASN][1000 genomes]
rs1732103	0.88[ASN][1000 genomes]
rs1882105	0.82[JPT][hapmap]
rs2141654	0.88[ASN][1000 genomes]
rs2178444	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2336081	0.80[CEU][hapmap]
rs28660352	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4974548	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4974598	0.99[ASN][1000 genomes]
rs4974599	0.89[ASN][1000 genomes]
rs6826688	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7679860	0.89[ASN][1000 genomes]
rs9884421	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 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	nsv1002097	chr4:1212573-1320086	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
12	nsv536986	chr4:1212573-1320086	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	esv1833544	chr4:1305962-1327941	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
29	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
30	esv3372793	chr4:1314128-1315122	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4974549	UVSSA	cis	Thyroid	GTEx
rs4974549	CTBP1	Cis_1M	lymphoblastoid	RTeQTL
rs4974549	UVSSA	cis	Whole Blood	GTEx
rs4974549	UVSSA	cis	Stomach	GTEx
rs4974549	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 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	chr4:1304400-1317200	Weak transcription	HSMMtube	muscle
3	chr4:1304400-1317400	Weak transcription	Fetal Brain Male	brain
4	chr4:1305000-1315200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:1305000-1327200	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr4:1305200-1315200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:1305200-1326600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr4:1305200-1330200	Weak transcription	Fetal Heart	heart
9	chr4:1305400-1316000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:1305800-1317400	Weak transcription	Right Atrium	heart
11	chr4:1306000-1323400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr4:1306200-1322200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:1306400-1315200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:1308800-1321200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:1309200-1330400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:1309400-1317000	Weak transcription	NH-A	brain
17	chr4:1310400-1316400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr4:1310600-1317400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr4:1310600-1321400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr4:1310800-1321800	Strong transcription	Primary T cells from cord blood	blood
21	chr4:1310800-1323200	Weak transcription	Psoas Muscle	Psoas
22	chr4:1311200-1321000	Weak transcription	Small Intestine	intestine
23	chr4:1311800-1321000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr4:1311800-1322400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:1312200-1317000	Weak transcription	Stomach Mucosa	stomach
26	chr4:1312200-1321800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr4:1312600-1316200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:1312800-1315400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:1312800-1315400	Weak transcription	Ovary	ovary
30	chr4:1312800-1315400	Weak transcription	NHLF	lung
31	chr4:1312800-1317000	Weak transcription	HUVEC	blood vessel
32	chr4:1312800-1317200	Weak transcription	NHDF-Ad	bronchial
33	chr4:1312800-1317400	Weak transcription	Brain Substantia Nigra	brain
34	chr4:1313000-1315400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr4:1313000-1315400	Weak transcription	Pancreas	Pancrea
36	chr4:1313000-1315600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr4:1313000-1315600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr4:1313000-1317400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr4:1313000-1318800	Weak transcription	Aorta	Aorta
40	chr4:1313200-1315400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:1313200-1316000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr4:1313200-1316000	Weak transcription	Colon Smooth Muscle	Colon
43	chr4:1313200-1316400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr4:1313200-1317000	Weak transcription	Hela-S3	cervix
45	chr4:1313200-1317600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr4:1313400-1315000	Weak transcription	GM12878-XiMat	blood
47	chr4:1313400-1315200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr4:1313400-1315200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr4:1313400-1315200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr4:1313400-1315200	Weak transcription	Esophagus	oesophagus

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