Variant report

Variant	rs3766222
Chromosome Location	chr1:47153122-47153123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:47152856-47153459	SK-N-SH	brain:	n/a	n/a
2	RXRA	chr1:47152885-47153338	SK-N-SH	brain:	n/a	chr1:47152891-47152905
3	NFIC	chr1:47152911-47153420	ECC-1	luminal epithelium:	n/a	chr1:47153133-47153150 chr1:47153134-47153150
4	POLR2A	chr1:47152985-47153334	SK-N-SH	brain:	n/a	n/a
5	EP300	chr1:47153041-47153329	SK-N-SH_RA	brain:	n/a	n/a
6	MEF2A	chr1:47152993-47153576	SK-N-SH	brain:	n/a	chr1:47153272-47153287 chr1:47153272-47153286 chr1:47153270-47153291 chr1:47153275-47153284 chr1:47153270-47153291 chr1:47153332-47153353 chr1:47153274-47153285 chr1:47153271-47153287 chr1:47153273-47153284
7	FOXP2	chr1:47153000-47153264	SK-N-MC	brain:	n/a	n/a
8	NFIC	chr1:47152821-47153538	SK-N-SH	brain:	n/a	chr1:47153133-47153150 chr1:47153134-47153150
9	NFIC	chr1:47152906-47153453	SK-N-SH	brain:	n/a	chr1:47153133-47153150 chr1:47153134-47153150
10	EP300	chr1:47152931-47153397	SK-N-SH_RA	brain:	n/a	n/a
11	TCF7L2	chr1:47153014-47153303	MCF-7	breast:	n/a	chr1:47153115-47153129
12	PBX3	chr1:47152982-47153417	SK-N-SH	brain:	n/a	n/a
13	TCF12	chr1:47152953-47153486	SK-N-SH	brain:	n/a	n/a
14	NFIC	chr1:47152779-47153476	ECC-1	luminal epithelium:	n/a	chr1:47153133-47153150 chr1:47153134-47153150

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47131372..47133587-chr1:47151853..47154733,2	MCF-7	breast:
2	chr1:47151853..47154363-chr1:47155084..47157704,2	K562	blood:

Variant related genes	Relation type
EFCAB14	TF binding region
ENSG00000159658	Chromatin interaction
ENSG00000233647	Chromatin interaction
ENSG00000123472	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10890410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10890414	0.97[ASN][1000 genomes]
rs11211332	0.90[EUR][1000 genomes]
rs11211343	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11211347	0.86[ASN][1000 genomes]
rs11801744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12059860	1.00[CEU][hapmap]
rs12060032	0.83[ASN][1000 genomes]
rs12562113	0.88[ASN][1000 genomes]
rs12566278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12568734	0.97[ASN][1000 genomes]
rs1258055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1258058	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258063	0.86[ASN][1000 genomes]
rs1258064	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258068	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258072	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1268714	0.88[ASN][1000 genomes]
rs1273237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13374909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1745376	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1933932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2146560	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2181412	0.88[ASN][1000 genomes]
rs2241863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2241864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2439442	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2476153	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2476155	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2476156	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2476157	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2476159	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2486160	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2486162	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3011290	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3766220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3766221	0.99[ASN][1000 genomes]
rs3766223	1.00[CHB][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56771521	0.97[ASN][1000 genomes]
rs57495753	0.97[ASN][1000 genomes]
rs582269	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs582323	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs582760	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs583649	0.94[ASN][1000 genomes]
rs58678760	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58920789	0.83[ASN][1000 genomes]
rs59479990	0.97[ASN][1000 genomes]
rs596794	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs597221	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60239027	0.83[ASN][1000 genomes]
rs604233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs604264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs611919	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs629412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs631368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs631840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs636082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs636122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs636424	0.96[ASN][1000 genomes]
rs648822	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs654544	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs655369	0.96[ASN][1000 genomes]
rs657166	0.96[ASN][1000 genomes]
rs6677350	1.00[CEU][hapmap]
rs669647	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs673134	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs675731	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs678466	0.85[ASN][1000 genomes]
rs683585	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs685862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs689300	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs723333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs724309	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs72896683	0.88[ASN][1000 genomes]
rs72900715	0.97[ASN][1000 genomes]
rs736188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription 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	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47134600-47157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:47138000-47157800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:47138200-47159400	Strong transcription	Placenta	Placenta
4	chr1:47138400-47158800	Strong transcription	Fetal Muscle Trunk	muscle
5	chr1:47138400-47159400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:47138800-47153200	Strong transcription	Fetal Muscle Leg	muscle
7	chr1:47138800-47158600	Strong transcription	Primary B cells from cord blood	blood
8	chr1:47139000-47159400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:47139200-47153400	Strong transcription	Dnd41	blood
10	chr1:47139200-47159400	Strong transcription	Brain Germinal Matrix	brain
11	chr1:47139200-47159800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:47139400-47159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:47139600-47159400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:47140000-47155400	Strong transcription	HSMM	muscle
15	chr1:47141200-47157800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:47142000-47159400	Strong transcription	K562	blood
18	chr1:47142000-47159800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:47142400-47158000	Strong transcription	HMEC	breast
20	chr1:47142600-47158200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:47142600-47159200	Strong transcription	GM12878-XiMat	blood
22	chr1:47142600-47159400	Strong transcription	NHEK	skin
23	chr1:47142800-47158800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:47142800-47159600	Strong transcription	Primary B cells from peripheral blood	blood
25	chr1:47142800-47159800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:47143200-47153600	Strong transcription	Brain Angular Gyrus	brain
27	chr1:47143200-47159400	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:47143200-47159400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:47143200-47159800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:47143600-47158400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:47143600-47159400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:47143800-47158200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:47143800-47159400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:47143800-47159400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:47143800-47159800	Strong transcription	Primary T cells from cord blood	blood
36	chr1:47143800-47171600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:47144000-47158200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:47144600-47159600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:47145000-47158000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:47145400-47153400	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr1:47145400-47158000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr1:47145400-47159000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:47145600-47157800	Strong transcription	NH-A	brain
44	chr1:47145800-47155800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:47145800-47158800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:47147000-47158200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
47	chr1:47147600-47158400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:47147800-47155800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:47147800-47157200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr1:47148000-47158000	Strong transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links