Variant report

Variant	rs3007704
Chromosome Location	chr1:151952075-151952076
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151811099..151813697-chr1:151950500..151952589,2	MCF-7	breast:
2	chr1:151881739..151884643-chr1:151951894..151953889,2	K562	blood:
3	chr1:151951145..151953064-chr1:151955721..151958103,2	K562	blood:
4	chr1:151952034..151953973-chr1:152006565..152009947,3	MCF-7	breast:
5	chr1:151951212..151953064-chr1:151955112..151957221,2	K562	blood:

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction
ENSG00000225556	Chromatin interaction
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1003107	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs10158030	0.82[ASW][hapmap];1.00[CHB][hapmap]
rs1038746	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1038748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10788813	1.00[CHB][hapmap]
rs10788816	1.00[CHB][hapmap]
rs10888453	1.00[CHB][hapmap]
rs11204911	1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs11204912	1.00[CHB][hapmap]
rs11204923	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs11578030	1.00[CHB][hapmap]
rs12723616	1.00[CHB][hapmap]
rs1352654	0.93[CHD][hapmap];0.90[GIH][hapmap]
rs1387834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1387835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473493	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473494	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473495	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1490187	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs1490191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1496037	1.00[CHB][hapmap]
rs1532132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1552605	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1552606	1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap]
rs1552607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1602245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1602246	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1602248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1602252	0.82[ASN][1000 genomes]
rs1602254	0.82[ASN][1000 genomes]
rs17583707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1826170	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1826171	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1826172	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1873311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1873312	1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap]
rs1967085	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2087550	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2338018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932564	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932567	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2932584	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932585	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2932588	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932591	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932595	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932596	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932597	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999509	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999511	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999515	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999518	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999519	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999520	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999522	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999523	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999524	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999525	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999527	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999530	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2999535	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2999536	1.00[CHB][hapmap]
rs2999537	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2999538	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2999547	1.00[CHB][hapmap]
rs2999551	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs2999552	1.00[CHB][hapmap]
rs2999555	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs2999558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3001979	1.00[CHB][hapmap]
rs3007671	1.00[CHB][hapmap]
rs3007672	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007676	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007679	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007690	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap]
rs3007692	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3007693	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3007699	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3122300	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3122301	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3134814	1.00[CHB][hapmap]
rs34370890	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4845385	1.00[CHB][hapmap]
rs4845388	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs4845393	1.00[CHB][hapmap]
rs4845660	1.00[CHB][hapmap]
rs4845664	1.00[CHB][hapmap]
rs61113720	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6587626	1.00[CHB][hapmap]
rs6587628	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs6587629	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs6587630	1.00[CHB][hapmap]
rs6587641	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6659029	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap]
rs6685291	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs6691350	1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap]
rs7529451	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[MEX][hapmap]
rs7532721	1.00[CHB][hapmap]
rs902314	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs902315	1.00[CHB][hapmap]
rs959945	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs971888	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9943225	1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases
6	nsv2855	chr1:151936470-151966381	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3007704	VPS72	cis	Stomach	GTEx
rs3007704	S100A10	cis	lymphoblastoid	seeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151934600-151953400	Weak transcription	Psoas Muscle	Psoas
2	chr1:151941000-151953200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:151941000-151953200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:151941000-151953400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:151941000-151953400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr1:151941000-151954800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:151941200-151952800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:151941200-151952800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:151941200-151953000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr1:151941200-151955200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:151941600-151961200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:151941800-151953000	Weak transcription	Lung	lung
13	chr1:151941800-151953600	Weak transcription	Gastric	stomach
14	chr1:151941800-151956200	Weak transcription	Pancreas	Pancrea
15	chr1:151943000-151953000	Weak transcription	Spleen	Spleen
16	chr1:151945400-151952400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:151945400-151953400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:151945600-151953000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:151945600-151953600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:151945600-151953800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:151945600-151953800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:151946000-151952600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:151946000-151954800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:151946000-151954800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:151946200-151952800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:151946200-151953000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:151946200-151953000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr1:151946200-151954800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:151946200-151954800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:151946200-151956200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:151946400-151952400	Weak transcription	HSMMtube	muscle
32	chr1:151946600-151957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr1:151946600-151958800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:151947600-151952400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:151947600-151953400	Enhancers	Placenta Amnion	Placenta Amnion
36	chr1:151948000-151956200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr1:151948400-151955200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:151949000-151953400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:151949200-151963200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:151949400-151953200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:151949600-151952400	Weak transcription	HUVEC	blood vessel
42	chr1:151949800-151952600	Weak transcription	NHLF	lung
43	chr1:151949800-151952800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:151949800-151952800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:151949800-151953400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:151949800-151953600	Weak transcription	Liver	Liver
47	chr1:151949800-151954800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:151949800-151957200	Weak transcription	Stomach Mucosa	stomach
49	chr1:151950000-151952600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:151950000-151952800	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links