Variant report

Variant	rs9375562
Chromosome Location	chr6:128675908-128675909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128668869..128672151-chr6:128674907..128677804,3	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10428737	1.00[MEX][hapmap]
rs11753971	1.00[CHD][hapmap]
rs11964875	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs11965122	0.85[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs11965141	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs11966128	0.85[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs1339189	0.85[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs1339196	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1416517	0.85[CEU][hapmap]
rs1538498	0.86[EUR][1000 genomes]
rs1612415	0.84[CEU][hapmap]
rs17055564	0.84[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs17055574	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs17055596	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs17055597	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs17055601	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs17055604	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs17055608	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs17055611	0.85[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs17055612	0.85[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs17055616	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs17055617	1.00[CHD][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs17055618	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs17055619	0.85[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs17055628	0.83[EUR][1000 genomes]
rs17055630	0.86[EUR][1000 genomes]
rs17055679	0.86[EUR][1000 genomes]
rs17055689	0.85[CEU][hapmap]
rs17055706	0.85[CEU][hapmap]
rs17055717	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs17055719	0.85[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs17055727	0.85[CEU][hapmap]
rs17055733	0.85[CEU][hapmap]
rs17055854	0.85[MEX][hapmap]
rs17343887	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs17353545	0.85[CEU][hapmap]
rs17430131	0.85[CEU][hapmap]
rs17430452	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs17456343	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs17456385	0.85[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs17456601	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1768353	1.00[CHD][hapmap]
rs1768357	1.00[CHD][hapmap]
rs1768360	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap]
rs2027311	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs4267969	0.86[EUR][1000 genomes]
rs4466261	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs55969073	0.86[EUR][1000 genomes]
rs56095177	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56241890	0.86[EUR][1000 genomes]
rs57318936	0.86[EUR][1000 genomes]
rs59132771	0.86[EUR][1000 genomes]
rs6913718	0.84[EUR][1000 genomes]
rs6931769	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs6933821	0.85[CEU][hapmap]
rs6939023	0.85[MEX][hapmap]
rs72967026	0.86[EUR][1000 genomes]
rs72967039	0.86[EUR][1000 genomes]
rs72967046	0.86[EUR][1000 genomes]
rs72967053	0.84[EUR][1000 genomes]
rs72967056	0.84[EUR][1000 genomes]
rs72967058	0.86[EUR][1000 genomes]
rs72967074	0.86[EUR][1000 genomes]
rs72967078	0.84[EUR][1000 genomes]
rs72967081	0.84[EUR][1000 genomes]
rs72967087	0.84[EUR][1000 genomes]
rs72967090	0.84[EUR][1000 genomes]
rs72969054	0.86[EUR][1000 genomes]
rs72969059	0.86[EUR][1000 genomes]
rs72969061	0.86[EUR][1000 genomes]
rs72969063	0.86[EUR][1000 genomes]
rs72969067	0.86[EUR][1000 genomes]
rs72969070	0.86[EUR][1000 genomes]
rs72969074	0.86[EUR][1000 genomes]
rs72969075	0.84[EUR][1000 genomes]
rs72969078	0.84[EUR][1000 genomes]
rs72969097	0.86[EUR][1000 genomes]
rs72969098	0.84[EUR][1000 genomes]
rs72971103	0.86[EUR][1000 genomes]
rs72972082	0.86[EUR][1000 genomes]
rs72972084	0.86[EUR][1000 genomes]
rs72972086	0.86[EUR][1000 genomes]
rs72974006	1.00[ASN][1000 genomes]
rs72974007	1.00[ASN][1000 genomes]
rs72974013	1.00[ASN][1000 genomes]
rs7764930	0.85[MEX][hapmap]
rs7771630	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs7773248	0.85[CEU][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs7776405	0.86[EUR][1000 genomes]
rs9321114	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs9372888	1.00[ASN][1000 genomes]
rs9402035	0.93[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491939	1.00[CEU][hapmap];0.86[MEX][hapmap]
rs953549	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS 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	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128649400-128678600	Weak transcription	HSMM	muscle
2	chr6:128661400-128677200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr6:128661600-128679400	Weak transcription	Osteobl	bone
4	chr6:128666000-128678600	Weak transcription	Left Ventricle	heart
5	chr6:128666000-128679400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:128668400-128677200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:128668600-128677200	Weak transcription	Small Intestine	intestine
8	chr6:128668600-128684200	Weak transcription	Fetal Kidney	kidney
9	chr6:128670400-128677400	Weak transcription	HSMMtube	muscle
10	chr6:128670400-128678600	Weak transcription	Brain Angular Gyrus	brain
11	chr6:128670400-128678600	Weak transcription	Brain Substantia Nigra	brain
12	chr6:128670600-128678000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:128671800-128678000	Weak transcription	Right Ventricle	heart
14	chr6:128672200-128678200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:128673000-128679000	Weak transcription	NH-A	brain
16	chr6:128673000-128681000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:128673000-128687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:128673200-128683200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:128674000-128684200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:128674000-128685800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:128674200-128679400	Weak transcription	Stomach Mucosa	stomach
22	chr6:128674600-128679400	Weak transcription	HepG2	liver
23	chr6:128674800-128676200	Enhancers	Fetal Intestine Large	intestine
24	chr6:128674800-128677600	Weak transcription	Fetal Heart	heart
25	chr6:128675000-128688000	Weak transcription	Gastric	stomach
26	chr6:128675800-128676200	Enhancers	Colon Smooth Muscle	Colon
27	chr6:128675800-128676200	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr6:128675800-128676200	Enhancers	Fetal Intestine Small	intestine
29	chr6:128675800-128676200	Enhancers	Fetal Lung	lung
30	chr6:128675800-128676200	Enhancers	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links