Variant report

Variant	rs17009859
Chromosome Location	chr12:83100495-83100496
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:83078166..83081005-chr12:83099084..83103387,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179104	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11115369	0.80[CHB][hapmap]
rs12313503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425493	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12578600	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13378007	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17009863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882522	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57227638	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57715118	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60454381	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6539680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7294774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7311617	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311886	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313780	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7315791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74106270	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7979455	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83082200-83102200	Weak transcription	Lung	lung
2	chr12:83082800-83102000	Weak transcription	NHDF-Ad	bronchial
3	chr12:83082800-83102200	Weak transcription	Pancreas	Pancrea
4	chr12:83083600-83101800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:83084000-83101400	Weak transcription	Fetal Kidney	kidney
6	chr12:83084600-83101200	Weak transcription	Fetal Stomach	stomach
7	chr12:83084800-83101400	Weak transcription	GM12878-XiMat	blood
8	chr12:83086000-83102200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:83086600-83122200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:83086800-83100800	Weak transcription	Fetal Heart	heart
11	chr12:83087200-83105600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:83087400-83101200	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:83087400-83106400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:83092800-83102200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:83093000-83101000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:83093200-83122400	Weak transcription	Gastric	stomach
17	chr12:83093400-83101200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:83093600-83101000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:83093800-83100800	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:83094600-83101000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:83095400-83106600	Weak transcription	Fetal Intestine Large	intestine
22	chr12:83096000-83102000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:83096000-83105800	Weak transcription	Fetal Intestine Small	intestine
24	chr12:83096200-83100800	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:83096200-83101200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:83098000-83121200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:83098800-83106800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr12:83099000-83101600	Weak transcription	Fetal Lung	lung
29	chr12:83099200-83122400	Weak transcription	Esophagus	oesophagus
30	chr12:83099400-83102200	Enhancers	Brain Substantia Nigra	brain
31	chr12:83099400-83103800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr12:83099600-83100600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:83099600-83100600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:83099600-83101200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:83099600-83101200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr12:83100400-83100600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:83100400-83100600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:83100400-83102200	Enhancers	Brain Anterior Caudate	brain
39	chr12:83100400-83103200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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