Variant report

Variant	rs7620750
Chromosome Location	chr3:119643181-119643182
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119636868..119639651-chr3:119641499..119644055,2	MCF-7	breast:
2	chr3:119636744..119638491-chr3:119642784..119644301,2	MCF-7	breast:

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10433404	0.89[YRI][hapmap]
rs10511395	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs1054191	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs10934500	0.85[YRI][hapmap]
rs10934502	0.89[YRI][hapmap]
rs10934503	0.88[YRI][hapmap]
rs10934505	0.89[YRI][hapmap]
rs10934506	0.89[YRI][hapmap]
rs10934507	0.95[YRI][hapmap]
rs1154595	0.82[CEU][hapmap]
rs1154596	0.82[CHB][hapmap]
rs1154597	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs11915717	0.89[YRI][hapmap]
rs11917714	0.82[YRI][hapmap]
rs11921053	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11929668	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs12494560	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12629015	0.89[YRI][hapmap]
rs12630592	0.82[CEU][hapmap]
rs12634476	0.89[YRI][hapmap]
rs12634889	0.81[YRI][hapmap]
rs12638973	0.88[YRI][hapmap]
rs13312998	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs13314595	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13321783	0.82[CEU][hapmap]
rs1574154	0.89[YRI][hapmap]
rs1579031	0.95[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16830683	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs16830689	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1719887	0.82[CHB][hapmap]
rs1719888	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs1719889	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1719894	0.82[CEU][hapmap]
rs1719895	0.82[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs17204878	0.82[CEU][hapmap]
rs1732165	0.84[ASN][1000 genomes]
rs1732169	0.84[ASN][1000 genomes]
rs1732170	0.82[CEU][hapmap]
rs182839	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs1870931	0.89[YRI][hapmap]
rs1903765	0.84[CEU][hapmap]
rs2037547	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2319398	0.82[CEU][hapmap]
rs2319399	0.82[CEU][hapmap]
rs2461816	0.84[CHD][hapmap]
rs2461827	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2472680	0.84[CHD][hapmap]
rs28516957	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28536662	0.82[CEU][hapmap]
rs3107669	0.82[CEU][hapmap]
rs3108749	0.82[CHB][hapmap];0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs334533	0.86[CEU][hapmap]
rs334534	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs334535	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs334536	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs334538	0.84[CHD][hapmap]
rs334559	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs334560	0.81[EUR][1000 genomes]
rs334561	0.82[CHB][hapmap]
rs334563	0.82[CEU][hapmap]
rs334566	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs3732361	0.82[CEU][hapmap]
rs4072520	0.94[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4261913	0.82[CEU][hapmap]
rs4340737	0.89[YRI][hapmap]
rs4438691	0.84[ASN][1000 genomes]
rs4450859	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4624596	0.89[YRI][hapmap]
rs4687890	0.82[CEU][hapmap]
rs4687893	0.82[CEU][hapmap]
rs4688042	0.89[YRI][hapmap]
rs4688043	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs4688046	0.89[YRI][hapmap]
rs4688047	0.89[YRI][hapmap]
rs4688054	0.89[YRI][hapmap]
rs56126162	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6438550	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs6438552	0.82[CEU][hapmap]
rs6438553	0.81[CEU][hapmap]
rs6438554	0.82[CHB][hapmap]
rs6438555	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs66650215	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6769435	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6770314	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6771023	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6774693	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6775397	0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6779828	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6781942	0.82[CEU][hapmap]
rs6782799	0.82[CEU][hapmap]
rs6784239	0.82[CHB][hapmap]
rs6784598	0.82[CEU][hapmap]
rs6785049	0.82[CEU][hapmap]
rs6785050	0.82[CHB][hapmap]
rs6790751	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6792572	0.82[CEU][hapmap]
rs6795653	0.82[CEU][hapmap]
rs6795874	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6797689	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs6800622	0.82[CEU][hapmap]
rs6802301	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6805251	0.81[CEU][hapmap]
rs6807868	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs6808874	0.89[YRI][hapmap]
rs7613197	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7617372	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7624540	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7633279	0.89[YRI][hapmap]
rs7636600	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7644234	0.86[CEU][hapmap]
rs7649661	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7650554	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs7652172	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9289138	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs968824	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs9784393	1.00[CHD][hapmap]
rs9813864	0.82[CEU][hapmap]
rs9829763	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs9851174	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9859778	0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9873477	0.82[CEU][hapmap]
rs9878473	0.82[CEU][hapmap]
rs9879992	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer 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 miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119546000-119663400	Weak transcription	Lung	lung
2	chr3:119597600-119659000	Weak transcription	Gastric	stomach
3	chr3:119608000-119643600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:119608200-119677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:119611200-119643400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:119611200-119667000	Weak transcription	Pancreas	Pancrea
7	chr3:119611400-119649400	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:119611400-119682200	Weak transcription	HSMMtube	muscle
9	chr3:119614200-119645200	Weak transcription	K562	blood
10	chr3:119625000-119668200	Weak transcription	Hela-S3	cervix
11	chr3:119628200-119643800	Weak transcription	Left Ventricle	heart
12	chr3:119628200-119655600	Weak transcription	Fetal Heart	heart
13	chr3:119628200-119663200	Weak transcription	Right Atrium	heart
14	chr3:119628400-119651000	Weak transcription	Right Ventricle	heart
15	chr3:119629600-119672200	Weak transcription	Fetal Stomach	stomach
16	chr3:119630200-119645400	Weak transcription	HUVEC	blood vessel
17	chr3:119630800-119663200	Weak transcription	Esophagus	oesophagus
18	chr3:119630800-119697400	Weak transcription	Thymus	Thymus
19	chr3:119631000-119644000	Weak transcription	Psoas Muscle	Psoas
20	chr3:119631000-119717000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:119631200-119647800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:119631200-119650400	Weak transcription	Small Intestine	intestine
23	chr3:119631400-119643200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:119631400-119644000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:119631400-119646200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:119631400-119660800	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:119631600-119656000	Weak transcription	NHEK	skin
28	chr3:119632200-119645400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:119633400-119655600	Weak transcription	Fetal Kidney	kidney
30	chr3:119634000-119656200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr3:119635000-119649400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:119635000-119652000	Weak transcription	Adipose Nuclei	Adipose
33	chr3:119635000-119665400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr3:119635000-119667000	Weak transcription	Placenta	Placenta
35	chr3:119635400-119664600	Weak transcription	HMEC	breast
36	chr3:119636200-119645400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:119636400-119667200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:119638800-119648200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:119638800-119655400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:119638800-119656000	Weak transcription	Primary T cells from cord blood	blood
41	chr3:119639400-119645200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:119639400-119651600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:119640000-119646800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:119640000-119649200	Weak transcription	Fetal Brain Female	brain
45	chr3:119640000-119649400	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:119640000-119650600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:119640000-119663800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr3:119640200-119655800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:119640400-119643800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:119640400-119643800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links