Variant report

Variant	rs12496176
Chromosome Location	chr3:159720653-159720654
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	chr3:159602113..159604329-chr3:159720537..159722903,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12486839	1.00[EUR][1000 genomes]
rs12487209	1.00[EUR][1000 genomes]
rs12487614	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12488038	1.00[EUR][1000 genomes]
rs12489264	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492679	0.96[ASN][1000 genomes]
rs12492730	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16830996	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16831029	0.83[EUR][1000 genomes]
rs2115174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2243115	0.88[YRI][hapmap]
rs2243136	0.87[YRI][hapmap]
rs34842858	0.96[ASN][1000 genomes]
rs35321606	0.96[ASN][1000 genomes]
rs480134	1.00[CHB][hapmap]
rs59249997	0.83[EUR][1000 genomes]
rs59972445	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6771983	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6784758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7427782	0.92[ASN][1000 genomes]
rs7427801	0.92[ASN][1000 genomes]
rs7427807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7429852	0.92[ASN][1000 genomes]
rs7625648	0.96[ASN][1000 genomes]
rs890914	0.88[YRI][hapmap]
rs9283612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9290052	0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs9290053	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9812698	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9812995	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9813028	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9816860	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9827531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9830969	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9834418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9835467	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9838248	0.94[ASN][1000 genomes]
rs9850910	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9851355	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9857045	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9862350	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9871440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9872678	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9873090	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9883287	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9968092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9968093	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9968095	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9968097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][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	nsv829769	chr3:159606913-159805282	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats 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 target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159707200-159724200	Weak transcription	Psoas Muscle	Psoas
2	chr3:159709800-159723800	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:159711600-159724200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr3:159712000-159729600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:159712200-159721400	Weak transcription	GM12878-XiMat	blood
6	chr3:159713000-159734800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:159713400-159721400	Weak transcription	NHLF	lung
8	chr3:159714400-159721000	Weak transcription	Osteobl	bone
9	chr3:159714400-159721200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:159714800-159722800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:159715000-159722800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:159718200-159721200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:159719000-159720800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:159719200-159721000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:159719400-159720800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:159719400-159721000	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr3:159719600-159720800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:159719600-159721800	Enhancers	Brain Substantia Nigra	brain
19	chr3:159719800-159721200	Weak transcription	HSMMtube	muscle
20	chr3:159719800-159724200	Weak transcription	Brain Anterior Caudate	brain
21	chr3:159720000-159724200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:159720000-159724200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:159720200-159721400	Weak transcription	NHDF-Ad	bronchial
24	chr3:159720200-159723800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:159720200-159724200	Weak transcription	Brain Hippocampus Middle	brain

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