Variant report

Variant	rs7957404
Chromosome Location	chr12:76241300-76241301
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	chr12:76234777..76238439-chr12:76239479..76242748,4	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10879990	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317066	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1275615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1275616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141707	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7134254	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7295719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305444	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7965922	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7972673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977768	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937240	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv832463	chr12:76136551-76316703	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv899315	chr12:76163309-76385096	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1041730	chr12:76198863-76331900	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7957404	PMF1	trans	parietal	SCAN
rs7957404	TSPAN8	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76228600-76250000	Weak transcription	Pancreas	Pancrea
2	chr12:76232200-76241400	Weak transcription	Fetal Stomach	stomach
3	chr12:76235600-76242600	Weak transcription	Left Ventricle	heart
4	chr12:76236000-76242000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:76236400-76242000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:76236800-76241400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:76238000-76242000	Weak transcription	Fetal Brain Male	brain
8	chr12:76238400-76241600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:76239400-76241600	Weak transcription	Ovary	ovary
10	chr12:76239400-76242000	Weak transcription	Brain Angular Gyrus	brain
11	chr12:76239400-76242000	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:76239600-76244600	Weak transcription	HepG2	liver
13	chr12:76239800-76241400	Weak transcription	HUVEC	blood vessel
14	chr12:76239800-76242400	Weak transcription	Fetal Brain Female	brain
15	chr12:76240000-76241400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:76240400-76241600	Weak transcription	Brain Germinal Matrix	brain
17	chr12:76240400-76242200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:76240400-76247400	Weak transcription	Aorta	Aorta
19	chr12:76240600-76241600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:76240800-76244600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:76241000-76242800	Enhancers	Fetal Lung	lung
22	chr12:76241200-76242200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:76241200-76243800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:76241200-76244000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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