Variant report

Variant	rs3800189
Chromosome Location	chr6:2228080-2228081
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	chr6:2225998..2228702-chr6:2230622..2232847,2	MCF-7	breast:
2	chr6:2226252..2228883-chr6:2229316..2232296,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10458134	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11242746	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11242747	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11242751	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11242753	0.84[AMR][1000 genomes]
rs12198593	0.90[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12198715	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12207377	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12209836	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12215717	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12216224	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12523924	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12525444	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12529507	0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs12529715	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12664420	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12665003	0.90[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13194365	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13195362	0.80[AMR][1000 genomes]
rs13196348	0.87[AMR][1000 genomes]
rs13196472	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13202573	0.80[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13206299	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13215846	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17134819	0.90[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2129178	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2295009	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs234913	0.83[CEU][hapmap]
rs35063859	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35410074	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58348518	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60015886	0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73342732	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9501817	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9647650	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS 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	25 gene(s)	inside rSNPs	diseases
3	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS 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	71 gene(s)	inside rSNPs	diseases
4	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
9	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
10	nsv830573	chr6:2120985-2263646	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv1022623	chr6:2199666-2267750	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv538100	chr6:2199666-2267750	ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv1022166	chr6:2199666-2320800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
14	nsv1017174	chr6:2213893-2340529	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
15	nsv1033201	chr6:2218647-2308518	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers 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	41 gene(s)	inside rSNPs	diseases
16	nsv538101	chr6:2218647-2308518	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2217400-2231400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:2217400-2231400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:2222600-2231400	Weak transcription	Aorta	Aorta
4	chr6:2222600-2244400	Weak transcription	Fetal Stomach	stomach
5	chr6:2222600-2244600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:2222800-2230000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:2222800-2243800	Weak transcription	Primary T cells from cord blood	blood
8	chr6:2223000-2229000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:2223000-2230000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:2223000-2230400	Enhancers	Stomach Mucosa	stomach
11	chr6:2223000-2231800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:2223200-2229200	Weak transcription	GM12878-XiMat	blood
13	chr6:2223200-2229800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:2223200-2229800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:2223200-2229800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:2223200-2230200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:2223200-2231200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:2223200-2231400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr6:2223200-2231400	Weak transcription	Spleen	Spleen
20	chr6:2223200-2231600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr6:2223200-2233000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:2223800-2231600	Weak transcription	Lung	lung
23	chr6:2226000-2229800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:2226000-2231200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:2226200-2229200	Weak transcription	HMEC	breast
26	chr6:2226200-2231200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:2226200-2231200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:2226200-2231200	Weak transcription	NH-A	brain
29	chr6:2226400-2229000	Weak transcription	Small Intestine	intestine
30	chr6:2226400-2231400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:2226600-2229600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:2226600-2231400	Weak transcription	Psoas Muscle	Psoas
33	chr6:2226600-2231400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr6:2226600-2231600	Weak transcription	HUVEC	blood vessel
35	chr6:2226800-2229400	Enhancers	Duodenum Mucosa	Duodenum
36	chr6:2226800-2231600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr6:2227000-2229400	Genic enhancers	HepG2	liver
38	chr6:2227200-2231200	Weak transcription	Osteobl	bone
39	chr6:2227200-2231400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:2227200-2236200	Weak transcription	Hela-S3	cervix
41	chr6:2227600-2228200	Enhancers	Pancreas	Pancrea
42	chr6:2227800-2228200	Enhancers	Colonic Mucosa	Colon
43	chr6:2227800-2239800	Weak transcription	Fetal Intestine Small	intestine
44	chr6:2228000-2228200	Enhancers	Right Atrium	heart
45	chr6:2228000-2228200	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr6:2228000-2228600	Enhancers	Gastric	stomach

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