Variant report

Variant	rs6581527
Chromosome Location	chr12:64421995-64421996
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	chr12:64421565..64423424-chr12:64425072..64428003,2	MCF-7	breast:
2	chr12:64419626..64423414-chr12:64423977..64427882,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255780	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10784376	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10784377	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10878099	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11175237	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11836824	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367875	0.96[CEU][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17710730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335389	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35136111	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35266586	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930087	0.81[CHB][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6421210	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581518	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581520	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6581521	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581522	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581524	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581525	0.80[ASW][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6581526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581528	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7295635	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]
rs7297628	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7299597	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308431	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7311377	0.81[CHB][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7312152	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7312345	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7316077	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958660	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7967578	0.82[AMR][1000 genomes];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];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7974633	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv747	chr12:64391572-64423998	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
3	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
rs6581527	GNS	cis	cerebellum	SCAN

Chromatin state (count:48 , 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	chr12:64383800-64425400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:64385000-64425600	Weak transcription	Left Ventricle	heart
5	chr12:64388800-64429800	Weak transcription	Pancreas	Pancrea
6	chr12:64398000-64425200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:64404600-64422400	Weak transcription	NH-A	brain
8	chr12:64408200-64422400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:64409400-64422000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:64409400-64429600	Weak transcription	Hela-S3	cervix
11	chr12:64409600-64422400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:64410000-64428600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:64411400-64422200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:64411400-64425600	Weak transcription	Fetal Intestine Small	intestine
15	chr12:64412000-64423800	Weak transcription	Aorta	Aorta
16	chr12:64413800-64422400	Weak transcription	NHEK	skin
17	chr12:64415000-64432400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:64415400-64422600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:64415800-64426000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:64416600-64422000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:64416600-64425400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:64416600-64432400	Weak transcription	Fetal Brain Female	brain
23	chr12:64417800-64422400	Weak transcription	HSMMtube	muscle
24	chr12:64418000-64422400	Weak transcription	HSMM	muscle
25	chr12:64418400-64422000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:64418600-64425200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:64418600-64456400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:64419000-64422600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:64419200-64422400	Weak transcription	HMEC	breast
30	chr12:64419600-64422000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:64419800-64422400	Weak transcription	Fetal Kidney	kidney
32	chr12:64419800-64424600	Weak transcription	Ovary	ovary
33	chr12:64419800-64428400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:64420000-64424600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:64420800-64422200	Enhancers	Brain Anterior Caudate	brain
36	chr12:64420800-64422400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:64420800-64422600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:64420800-64422800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:64420800-64424800	Enhancers	NHDF-Ad	bronchial
40	chr12:64420800-64424800	Enhancers	Osteobl	bone
41	chr12:64421000-64422200	Enhancers	Brain Cingulate Gyrus	brain
42	chr12:64421200-64422200	Weak transcription	Brain Substantia Nigra	brain
43	chr12:64421200-64423400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:64421400-64422400	Weak transcription	Adipose Nuclei	Adipose
45	chr12:64421400-64423200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:64421600-64422400	Weak transcription	A549	lung
47	chr12:64421800-64422200	Weak transcription	NHLF	lung
48	chr12:64421800-64422800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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