Variant report

Variant	rs17009856
Chromosome Location	chr12:83086170-83086171
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	chr12:83079543..83083074-chr12:83085664..83088459,4	MCF-7	breast:
2	chr12:83080249..83082936-chr12:83085734..83087836,2	K562	blood:

Variant related genes	Relation type
ENSG00000179104	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10862497	0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11115339	0.81[AMR][1000 genomes]
rs11115342	1.00[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11115348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11115353	0.88[EUR][1000 genomes]
rs11115355	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11609532	0.92[EUR][1000 genomes]
rs11610988	0.80[EUR][1000 genomes]
rs11613168	0.80[EUR][1000 genomes]
rs11614435	0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs11615763	0.80[EUR][1000 genomes]
rs11615765	0.80[EUR][1000 genomes]
rs12305736	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307168	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422405	0.82[CEU][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12423043	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12426166	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12579483	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs13377925	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17009812	0.84[EUR][1000 genomes]
rs17009851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17009854	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17009882	0.82[EUR][1000 genomes]
rs17009885	0.82[EUR][1000 genomes]
rs17009891	0.80[EUR][1000 genomes]
rs17009893	0.80[EUR][1000 genomes]
rs17009899	0.80[EUR][1000 genomes]
rs1922576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1922579	0.91[EUR][1000 genomes]
rs4620789	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4882428	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55657485	0.92[EUR][1000 genomes]
rs56298822	0.95[EUR][1000 genomes]
rs56396658	0.92[EUR][1000 genomes]
rs61485473	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539683	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7134747	0.84[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7134766	0.95[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7135486	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72615654	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7294890	0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7303469	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7313778	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73354481	0.84[EUR][1000 genomes]
rs74106267	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7954021	0.81[AMR][1000 genomes]
rs7961953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7975647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9805078	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv559541	chr12:82715210-83108395	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv899348	chr12:82744187-83169297	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv427917	chr12:82917031-83279712	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv899349	chr12:82931646-83114286	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv3348300	chr12:83079532-83086951	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83082200-83089200	Weak transcription	Esophagus	oesophagus
2	chr12:83082200-83102200	Weak transcription	Lung	lung
3	chr12:83082400-83086800	Weak transcription	Adipose Nuclei	Adipose
4	chr12:83082400-83089000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:83082600-83086400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr12:83082600-83087200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:83082600-83088600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:83082600-83088800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:83082600-83094600	Weak transcription	Left Ventricle	heart
10	chr12:83082800-83088200	Weak transcription	HMEC	breast
11	chr12:83082800-83089400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr12:83082800-83095200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:83082800-83099400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:83082800-83102000	Weak transcription	NHDF-Ad	bronchial
15	chr12:83082800-83102200	Weak transcription	Pancreas	Pancrea
16	chr12:83083000-83086200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:83083000-83089200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:83083000-83089400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:83083000-83089400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:83083000-83092400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:83083600-83086600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:83083600-83101800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:83083800-83088200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:83084000-83086400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:83084000-83087000	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:83084000-83092000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:83084000-83101400	Weak transcription	Fetal Kidney	kidney
28	chr12:83084200-83086200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr12:83084200-83086800	Enhancers	Brain Germinal Matrix	brain
30	chr12:83084400-83087200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:83084600-83086200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:83084600-83093400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:83084600-83101200	Weak transcription	Fetal Stomach	stomach
34	chr12:83084800-83086400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:83084800-83088800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr12:83084800-83089600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr12:83084800-83090200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr12:83084800-83092800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr12:83084800-83101400	Weak transcription	GM12878-XiMat	blood
40	chr12:83085200-83091600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr12:83085600-83086400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:83085800-83086200	Enhancers	Brain Hippocampus Middle	brain
43	chr12:83085800-83086200	Bivalent Enhancer	Fetal Brain Male	brain
44	chr12:83085800-83086200	Enhancers	Fetal Brain Female	brain
45	chr12:83085800-83086400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:83085800-83086600	Enhancers	Brain Substantia Nigra	brain
47	chr12:83085800-83086800	Enhancers	Brain Anterior Caudate	brain
48	chr12:83085800-83086800	Enhancers	Fetal Heart	heart
49	chr12:83085800-83087000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:83085800-83087200	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links