Variant report

Variant	rs7629156
Chromosome Location	chr3:111462570-111462571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111452077..111454237-chr3:111460686..111462940,2	K562	blood:
2	chr3:111459238..111460946-chr3:111462346..111465281,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10804492	1.00[ASW][hapmap];1.00[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];1.00[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]
rs11711582	0.81[CHD][hapmap]
rs11922220	0.85[CEU][hapmap]
rs11929568	0.88[ASW][hapmap];0.89[LWK][hapmap]
rs12490337	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12495513	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs12632878	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1355769	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4325897	0.85[CEU][hapmap]
rs4557129	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682299	0.81[CHD][hapmap]
rs4682302	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438003	0.81[CHD][hapmap]
rs6782962	0.90[CEU][hapmap]
rs6784441	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs6788543	0.81[CHD][hapmap]
rs6794420	0.89[LWK][hapmap]
rs6796087	0.81[CHD][hapmap]
rs6796976	0.89[LWK][hapmap]
rs6801225	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs955382	0.96[AMR][1000 genomes];1.00[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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7629156	GAP43	cis	parietal	SCAN
rs7629156	C3orf17	cis	parietal	SCAN
rs7629156	CD200	cis	cerebellum	SCAN
rs7629156	SAT2	trans	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111454800-111464400	Weak transcription	Placenta	Placenta
2	chr3:111456200-111465600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:111458000-111467000	Weak transcription	Right Ventricle	heart
4	chr3:111458600-111464400	Weak transcription	Psoas Muscle	Psoas
5	chr3:111458600-111467200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:111458800-111464800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:111458800-111466800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:111459000-111466400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:111459000-111466400	Weak transcription	NHDF-Ad	bronchial
10	chr3:111459000-111466600	Weak transcription	Stomach Mucosa	stomach
11	chr3:111459200-111464600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:111459200-111466400	Weak transcription	Gastric	stomach
13	chr3:111459200-111466600	Weak transcription	Osteobl	bone
14	chr3:111459400-111465600	Weak transcription	HepG2	liver
15	chr3:111459800-111464200	Weak transcription	Hela-S3	cervix
16	chr3:111460200-111464800	Weak transcription	A549	lung
17	chr3:111460400-111464200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:111460400-111464400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:111460400-111464600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:111460400-111464600	Weak transcription	HMEC	breast
21	chr3:111460600-111464600	Weak transcription	NHEK	skin
22	chr3:111461800-111463000	Enhancers	Adipose Nuclei	Adipose
23	chr3:111462000-111462600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr3:111462000-111462600	Enhancers	Fetal Kidney	kidney
25	chr3:111462000-111463200	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr3:111462200-111462600	Enhancers	Stomach Smooth Muscle	stomach
27	chr3:111462200-111463200	Enhancers	Rectal Smooth Muscle	rectum
28	chr3:111462200-111463800	Enhancers	Colon Smooth Muscle	Colon
29	chr3:111462400-111466800	Weak transcription	Liver	Liver

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