Variant report

Variant	rs4620684
Chromosome Location	chr11:16178626-16178627
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:16171743..16174574-chr11:16176679..16178983,2	MCF-7	breast:
2	chr11:16178415..16182237-chr11:16182900..16185853,4	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10741688	0.91[CEU][hapmap]
rs10832552	0.95[ASN][1000 genomes]
rs10832555	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs10832556	0.88[EUR][1000 genomes]
rs10832557	0.88[EUR][1000 genomes]
rs11023859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11023860	0.96[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs1349984	0.89[EUR][1000 genomes]
rs1349985	0.89[EUR][1000 genomes]
rs1349986	0.92[EUR][1000 genomes]
rs1356647	0.96[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs1378305	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs1455103	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1455104	0.80[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs1455109	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1455111	0.96[CEU][hapmap];0.83[GIH][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs1455113	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1455114	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1455115	0.87[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.80[LWK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs1455117	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1455118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1914875	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1949482	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1949483	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2014828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs2054095	0.88[EUR][1000 genomes]
rs2124202	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2168253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3903292	0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4545520	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs4617548	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs6486276	0.89[EUR][1000 genomes]
rs6486277	0.88[EUR][1000 genomes]
rs6486278	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6486279	0.88[EUR][1000 genomes]
rs7102224	0.88[EUR][1000 genomes]
rs7108091	0.96[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs7112473	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7114017	0.88[EUR][1000 genomes]
rs7118395	0.96[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs7125634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7131157	0.83[EUR][1000 genomes]
rs7926424	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs7931734	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs7941496	0.92[CEU][hapmap];0.98[TSI][hapmap]
rs7950736	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs9651573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs978294	0.96[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv553562	chr11:16112180-16220289	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv529731	chr11:16122782-16468170	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4620684	DKFZp686O24166	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16172400-16191400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr11:16172600-16191400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr11:16174200-16191200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:16174800-16180000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:16175000-16180800	Enhancers	NHEK	skin
6	chr11:16175200-16180600	Enhancers	HMEC	breast
7	chr11:16175400-16179000	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr11:16177000-16180000	Weak transcription	Hela-S3	cervix
9	chr11:16177200-16179800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr11:16177600-16181000	Enhancers	A549	lung
11	chr11:16177600-16187800	Weak transcription	Fetal Intestine Small	intestine
12	chr11:16177800-16179000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:16178000-16185200	Weak transcription	Fetal Intestine Large	intestine
14	chr11:16178400-16178800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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