Variant report

Variant	rs2141654
Chromosome Location	chr4:1284888-1284889
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:1003302..1006299-chr4:1283517..1285282,2	K562	blood:
2	chr4:1280840..1286312-chr4:1338111..1343712,9	K562	blood:
3	chr4:1280807..1287593-chr4:1339102..1342185,6	K562	blood:
4	chr4:1280977..1287340-chr4:1335495..1344055,33	MCF-7	breast:
5	chr4:1284419..1287813-chr4:1334118..1338051,4	MCF-7	breast:
6	chr4:1238004..1246805-chr4:1279798..1288475,25	K562	blood:
7	chr4:1238004..1248980-chr4:1275065..1286840,30	K562	blood:
8	chr4:964532..968039-chr4:1281587..1285155,3	K562	blood:
9	chr4:1242091..1248517-chr4:1279714..1285424,16	MCF-7	breast:
10	chr4:1282437..1287650-chr4:1338224..1344043,13	MCF-7	breast:
11	chr4:1236833..1250005-chr4:1276188..1292579,54	MCF-7	breast:
12	chr4:1283242..1284963-chr4:1794686..1797481,2	K562	blood:
13	chr17:7387016..7389305-chr4:1283766..1286186,2	MCF-7	breast:
14	chr4:1284288..1286116-chr4:1712306..1714315,2	K562	blood:
15	chr4:1230672..1232310-chr4:1283727..1285762,2	K562	blood:
16	chr4:1078292..1079927-chr4:1283722..1285747,2	MCF-7	breast:
17	chr4:491408..492966-chr4:1283659..1285933,2	K562	blood:
18	chr4:1159320..1162756-chr4:1282339..1286135,5	K562	blood:
19	chr4:1005260..1007354-chr4:1282653..1285834,3	MCF-7	breast:
20	chr4:1271525..1273880-chr4:1284535..1286045,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000068078	Chromatin interaction
ENSG00000196810	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000182903	Chromatin interaction
ENSG00000159692	Chromatin interaction
ENSG00000145214	Chromatin interaction
ENSG00000163945	Chromatin interaction
ENSG00000273179	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000127418	Chromatin interaction
ENSG00000163950	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10016557	0.95[CEU][hapmap]
rs11247992	0.87[ASN][1000 genomes]
rs1137789	0.92[CEU][hapmap]
rs11727297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250120	0.82[AMR][1000 genomes]
rs1250122	0.82[AMR][1000 genomes]
rs12641735	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13129712	0.90[ASN][1000 genomes]
rs13147602	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs1680030	0.89[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs1680056	1.00[YRI][hapmap]
rs1680080	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1680083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732111	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1882105	0.91[CHB][hapmap]
rs2178444	0.85[ASN][1000 genomes]
rs2293634	0.81[ASN][1000 genomes]
rs2336081	1.00[CEU][hapmap]
rs28660352	0.89[ASN][1000 genomes]
rs3755920	0.88[CHB][hapmap]
rs4974548	0.87[ASN][1000 genomes]
rs4974549	0.88[ASN][1000 genomes]
rs4974598	0.89[ASN][1000 genomes]
rs4974611	1.00[CEU][hapmap]
rs4974612	0.92[CEU][hapmap]
rs4974613	0.83[CEU][hapmap]
rs4974620	0.80[CEU][hapmap]
rs56903463	0.88[EUR][1000 genomes]
rs6599308	0.96[CEU][hapmap]
rs6599309	0.88[CEU][hapmap]
rs6826688	0.82[ASN][1000 genomes]
rs6838561	0.88[CEU][hapmap]
rs6851528	0.81[ASN][1000 genomes]
rs7684445	0.80[CEU][hapmap]
rs7695691	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9884421	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 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	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription 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	59 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	esv1811773	chr4:1228251-1287474	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
15	esv1800629	chr4:1228451-1287274	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers 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
16	esv1812851	chr4:1228451-1287274	Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
17	esv1823612	chr4:1228451-1287274	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
18	esv1825633	chr4:1228451-1287274	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS 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
19	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
20	nsv461156	chr4:1254930-1312394	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers 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	16 gene(s)	inside rSNPs	diseases
21	nsv593299	chr4:1254930-1312394	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
22	esv1798897	chr4:1265740-1287474	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
23	esv1833294	chr4:1265740-1287474	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
24	esv1829934	chr4:1265940-1287274	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
25	nsv593300	chr4:1272664-1312394	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
26	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
27	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
28	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
29	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
30	esv3402251	chr4:1282477-1285325	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
31	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2141654	UVSSA	cis	Stomach	GTEx
rs2141654	UVSSA	cis	Thyroid	GTEx
rs2141654	CTBP1	Cis_1M	lymphoblastoid	RTeQTL
rs2141654	CTBP1-AS2	cis	Thyroid	GTEx
rs2141654	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx
rs2141654	MGC21675	cis	multi-tissue	Pritchard
rs2141654	UVSSA	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1282400-1285200	Active TSS	H9 Cell Line	embryonic stem cell
2	chr4:1282600-1285000	Active TSS	K562	blood
3	chr4:1282600-1285200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr4:1282600-1285400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:1282600-1285400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr4:1282600-1285400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr4:1282600-1285600	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr4:1282800-1285000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:1282800-1285000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:1282800-1285000	Active TSS	GM12878-XiMat	blood
11	chr4:1282800-1285000	Active TSS	HMEC	breast
12	chr4:1283000-1285000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:1283000-1285000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:1283000-1285000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:1283000-1285000	Active TSS	Fetal Intestine Small	intestine
16	chr4:1283000-1285000	Active TSS	NHDF-Ad	bronchial
17	chr4:1283000-1285000	Active TSS	NHLF	lung
18	chr4:1283000-1285200	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr4:1283000-1285400	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr4:1283200-1285200	Active TSS	Fetal Intestine Large	intestine
21	chr4:1284200-1285000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr4:1284200-1285000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:1284200-1285200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr4:1284200-1285200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr4:1284200-1285200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr4:1284200-1285200	Flanking Active TSS	Liver	Liver
27	chr4:1284200-1285400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr4:1284200-1285400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr4:1284200-1285400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:1284200-1285400	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr4:1284200-1285400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr4:1284200-1285400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr4:1284200-1285600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr4:1284200-1285600	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr4:1284200-1285800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:1284200-1286000	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr4:1284400-1285000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr4:1284400-1285000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:1284400-1285000	Flanking Active TSS	Brain Substantia Nigra	brain
40	chr4:1284400-1285000	Flanking Active TSS	Fetal Muscle Trunk	muscle
41	chr4:1284400-1285000	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr4:1284400-1285000	Flanking Active TSS	Fetal Stomach	stomach
43	chr4:1284400-1285200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:1284400-1285200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr4:1284400-1285200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr4:1284400-1285200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr4:1284400-1285200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:1284400-1285200	Flanking Active TSS	Esophagus	oesophagus
49	chr4:1284400-1285200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr4:1284400-1285200	Flanking Active TSS	Fetal Heart	heart

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