Variant report

Variant	rs7295635
Chromosome Location	chr12:64425423-64425424
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	chr12:64237304..64239476-chr12:64424891..64426645,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196935	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10784376	0.83[EUR][1000 genomes]
rs10784377	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs10878099	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11175237	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11836824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367875	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17710730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335389	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35136111	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35266586	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930087	0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs6421210	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581518	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581520	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6581521	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581522	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581524	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581528	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7297628	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7299597	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][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]
rs7308431	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7311377	0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs7312152	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7312345	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7316077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958660	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7967578	0.83[EUR][1000 genomes]
rs7970430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971280	0.96[CEU][hapmap];0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7974633	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978183	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3351487	chr12:64420364-64763950	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7295635	GNS	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64380200-64433000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:64382800-64432800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:64385000-64425600	Weak transcription	Left Ventricle	heart
4	chr12:64388800-64429800	Weak transcription	Pancreas	Pancrea
5	chr12:64409400-64429600	Weak transcription	Hela-S3	cervix
6	chr12:64410000-64428600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:64411400-64425600	Weak transcription	Fetal Intestine Small	intestine
8	chr12:64415000-64432400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:64415800-64426000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:64416600-64432400	Weak transcription	Fetal Brain Female	brain
11	chr12:64418600-64456400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:64419800-64428400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:64422600-64425800	Weak transcription	Brain Substantia Nigra	brain
14	chr12:64422800-64433200	Weak transcription	Small Intestine	intestine
15	chr12:64423000-64425600	Weak transcription	NHEK	skin
16	chr12:64423000-64432600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:64423000-64433000	Weak transcription	HMEC	breast
18	chr12:64423200-64429200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:64423400-64425600	Weak transcription	A549	lung
20	chr12:64423400-64428800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:64423400-64429800	Weak transcription	HSMM	muscle
22	chr12:64423400-64430000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:64423400-64433000	Weak transcription	Fetal Stomach	stomach
24	chr12:64423400-64433000	Weak transcription	HSMMtube	muscle
25	chr12:64423600-64426000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:64423600-64426000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:64423600-64429000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:64424600-64432800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:64424800-64429600	Weak transcription	NHDF-Ad	bronchial
30	chr12:64424800-64429800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:64424800-64429800	Weak transcription	Osteobl	bone
32	chr12:64424800-64430200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:64424800-64432400	Weak transcription	Stomach Mucosa	stomach
34	chr12:64424800-64432600	Weak transcription	NHLF	lung
35	chr12:64425000-64427600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:64425200-64425800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:64425200-64426400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
38	chr12:64425200-64426400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:64425400-64426400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:64425400-64426400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:64425400-64426400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:64425400-64427200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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