Variant report

Variant	rs1006561
Chromosome Location	chr17:16412342-16412343
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16410959..16413374-chr17:16417428..16419543,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1006958	1.00[TSI][hapmap]
rs10438732	1.00[TSI][hapmap]
rs16959784	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16959831	1.00[EUR][1000 genomes]
rs16959832	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16959849	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28375510	1.00[EUR][1000 genomes]
rs28375681	1.00[EUR][1000 genomes]
rs28481713	1.00[EUR][1000 genomes]
rs28482815	1.00[EUR][1000 genomes]
rs57062804	1.00[EUR][1000 genomes]
rs57088651	1.00[EUR][1000 genomes]
rs57432974	1.00[EUR][1000 genomes]
rs6502511	1.00[EUR][1000 genomes]
rs6502512	1.00[EUR][1000 genomes]
rs7211497	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7212777	1.00[EUR][1000 genomes]
rs7214389	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7218171	1.00[EUR][1000 genomes]
rs7218177	1.00[EUR][1000 genomes]
rs7220797	1.00[EUR][1000 genomes]
rs7220867	1.00[EUR][1000 genomes]
rs7221073	1.00[EUR][1000 genomes]
rs7222107	1.00[EUR][1000 genomes]
rs73282666	1.00[EUR][1000 genomes]
rs73282673	1.00[EUR][1000 genomes]
rs73282675	1.00[EUR][1000 genomes]
rs73282678	1.00[EUR][1000 genomes]
rs73980200	1.00[EUR][1000 genomes]
rs8066377	1.00[EUR][1000 genomes]
rs8068846	1.00[EUR][1000 genomes]
rs8069772	1.00[EUR][1000 genomes]
rs8069951	1.00[EUR][1000 genomes]
rs9890785	1.00[EUR][1000 genomes]
rs9899370	1.00[EUR][1000 genomes]
rs9900136	1.00[EUR][1000 genomes]
rs9900601	1.00[EUR][1000 genomes]
rs9902632	1.00[EUR][1000 genomes]
rs9912467	1.00[EUR][1000 genomes]
rs9912759	1.00[EUR][1000 genomes]
rs9916250	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
6	nsv1061463	chr17:16245878-16490691	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
7	nsv543216	chr17:16245878-16490691	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
8	nsv428668	chr17:16265210-16455285	Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
9	nsv1063941	chr17:16357086-16424098	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16409000-16415800	Weak transcription	Colonic Mucosa	Colon
2	chr17:16409000-16417600	Weak transcription	Gastric	stomach
3	chr17:16411000-16412800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr17:16411200-16413200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr17:16411200-16413600	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr17:16411200-16420400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr17:16411400-16412400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr17:16411400-16412800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:16411400-16412800	Enhancers	Fetal Muscle Leg	muscle
10	chr17:16411600-16412400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr17:16411800-16413600	Weak transcription	Primary B cells from cord blood	blood
12	chr17:16411800-16415400	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr17:16412000-16412400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr17:16412000-16414800	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links