Variant report

Variant	rs6486334
Chromosome Location	chr11:17015557-17015558
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	chr11:17014688..17017015-chr11:17017625..17019275,2	MCF-7	breast:
2	chr11:17007364..17008907-chr11:17013978..17016924,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10741719	1.00[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs10741720	1.00[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs10766366	0.90[EUR][1000 genomes]
rs10766367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10766368	0.84[ASN][1000 genomes]
rs10766370	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs10832707	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10832709	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10832710	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832713	1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10832716	0.80[AFR][1000 genomes]
rs10832717	0.81[AFR][1000 genomes]
rs10832721	0.92[YRI][hapmap]
rs11024101	0.80[ASN][1000 genomes]
rs11024102	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs11024103	0.92[ASN][1000 genomes]
rs11024110	0.81[ASN][1000 genomes]
rs11529141	0.92[EUR][1000 genomes]
rs12575487	0.84[ASN][1000 genomes]
rs1468489	1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2302207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2353369	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4237715	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4237716	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs4351794	0.95[LWK][hapmap];0.82[YRI][hapmap]
rs4469869	0.91[EUR][1000 genomes]
rs4562807	0.81[AFR][1000 genomes]
rs4756882	0.84[AFR][1000 genomes]
rs4756883	0.81[AFR][1000 genomes]
rs4757468	0.90[EUR][1000 genomes]
rs4757470	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs4757472	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4757473	0.95[CEU][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs4757474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757475	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757476	0.92[EUR][1000 genomes]
rs4757479	0.81[AFR][1000 genomes]
rs4757482	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4757484	1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4757487	0.96[YRI][hapmap]
rs4757489	1.00[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap]
rs4757490	0.95[LWK][hapmap];0.82[YRI][hapmap]
rs6486332	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6486333	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6486335	1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6486341	0.96[YRI][hapmap]
rs7118307	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7122802	0.92[EUR][1000 genomes]
rs7127818	0.82[JPT][hapmap]
rs7928955	0.80[AFR][1000 genomes]
rs7930890	0.88[AFR][1000 genomes]
rs7931025	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs7933984	1.00[LWK][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs7934567	0.92[EUR][1000 genomes]
rs7937479	0.84[AFR][1000 genomes]
rs7940499	0.97[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7944490	0.92[EUR][1000 genomes]
rs7947297	1.00[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832077	chr11:16834545-17059176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6486334	INSC	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17004800-17034200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:17006400-17034000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:17008400-17016000	Weak transcription	Thymus	Thymus
4	chr11:17009400-17015800	Weak transcription	Left Ventricle	heart
5	chr11:17009400-17032600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:17009600-17017600	Weak transcription	Ovary	ovary
7	chr11:17009800-17018000	Weak transcription	Spleen	Spleen
8	chr11:17009800-17018800	Weak transcription	A549	lung
9	chr11:17009800-17030000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr11:17009800-17032600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr11:17009800-17032600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:17010000-17015600	Weak transcription	Colonic Mucosa	Colon
13	chr11:17010000-17015800	Weak transcription	Lung	lung
14	chr11:17010000-17019000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:17010000-17023000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:17011600-17015600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:17012400-17024200	Enhancers	Stomach Mucosa	stomach
18	chr11:17012600-17017000	Weak transcription	Brain Hippocampus Middle	brain
19	chr11:17013400-17016000	Enhancers	Fetal Heart	heart
20	chr11:17013400-17018000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr11:17013400-17033800	Weak transcription	Brain Substantia Nigra	brain
22	chr11:17013800-17015600	Weak transcription	Esophagus	oesophagus
23	chr11:17014000-17017600	Weak transcription	Brain Anterior Caudate	brain
24	chr11:17014000-17023400	Weak transcription	Fetal Stomach	stomach
25	chr11:17014000-17025000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:17014200-17019200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr11:17014200-17021200	Genic enhancers	Fetal Intestine Small	intestine
28	chr11:17014200-17021400	Enhancers	Fetal Intestine Large	intestine
29	chr11:17014400-17016000	Enhancers	Fetal Kidney	kidney
30	chr11:17014400-17018600	Enhancers	Duodenum Mucosa	Duodenum
31	chr11:17014400-17019000	Enhancers	Liver	Liver
32	chr11:17014600-17015800	Enhancers	Right Atrium	heart
33	chr11:17014600-17017800	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr11:17014600-17019000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:17014600-17021000	Enhancers	Pancreas	Pancrea
36	chr11:17014800-17018600	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr11:17015000-17016000	Enhancers	Adipose Nuclei	Adipose
38	chr11:17015000-17024800	Enhancers	Gastric	stomach
39	chr11:17015200-17016800	Weak transcription	Right Ventricle	heart
40	chr11:17015200-17017800	Weak transcription	Small Intestine	intestine
41	chr11:17015400-17016400	Enhancers	HepG2	liver

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