Variant report

Variant	rs7612363
Chromosome Location	chr3:178720228-178720229
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11711320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720081	0.94[EUR][1000 genomes]
rs1542	0.82[JPT][hapmap]
rs2699887	0.80[CEU][hapmap]
rs2699905	0.80[CEU][hapmap]
rs4245914	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4279147	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4280676	0.94[EUR][1000 genomes]
rs4315724	0.94[EUR][1000 genomes]
rs4325967	0.83[ASN][1000 genomes]
rs4337680	0.94[EUR][1000 genomes]
rs4377525	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4395442	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417911	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4425305	1.00[ASN][1000 genomes]
rs4469018	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4501160	0.94[EUR][1000 genomes]
rs4505756	0.94[EUR][1000 genomes]
rs4522816	0.91[EUR][1000 genomes]
rs4525914	0.91[EUR][1000 genomes]
rs4552405	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579062	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4607155	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4626139	0.94[EUR][1000 genomes]
rs4632588	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4637331	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4955796	0.94[EUR][1000 genomes]
rs4955802	0.91[EUR][1000 genomes]
rs4955807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4955810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56115013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56154408	0.91[EUR][1000 genomes]
rs6443607	0.91[EUR][1000 genomes]
rs6443614	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6443617	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6443618	0.84[AMR][1000 genomes]
rs6772028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6784495	0.85[CEU][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs6789706	0.90[EUR][1000 genomes]
rs6790867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793893	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6794165	0.86[AMR][1000 genomes]
rs6794956	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6795238	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6800015	1.00[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6804084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7429173	0.94[EUR][1000 genomes]
rs7633318	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7639391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7643052	0.91[EUR][1000 genomes]
rs7651510	0.94[EUR][1000 genomes]
rs7652668	0.93[EUR][1000 genomes]
rs7652946	0.94[EUR][1000 genomes]
rs9830482	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9831543	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs9835752	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9835765	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9846511	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9860318	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9860749	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9878734	0.91[ASN][1000 genomes]
rs9879637	0.94[EUR][1000 genomes]
rs9880749	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9968179	0.85[CEU][hapmap];0.81[TSI][hapmap]

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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7612363	ATP11B	cis	parietal	SCAN
rs7612363	KCNMB3	cis	parietal	SCAN
rs7612363	YEATS2	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178708600-178726200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:178708800-178737800	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:178709200-178724400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:178709400-178721600	Weak transcription	Primary B cells from cord blood	blood
5	chr3:178709600-178724800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:178711800-178722600	Weak transcription	Gastric	stomach
7	chr3:178713000-178723000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:178713200-178725000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:178715200-178721800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:178715800-178723000	Strong transcription	HSMM	muscle
11	chr3:178716400-178755000	Weak transcription	Pancreas	Pancrea
12	chr3:178716800-178720800	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:178717000-178720600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:178717400-178744400	Weak transcription	HMEC	breast
15	chr3:178717800-178722800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:178718600-178722600	Weak transcription	Osteobl	bone
17	chr3:178718800-178720400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:178718800-178724400	Weak transcription	NHLF	lung
19	chr3:178719000-178720400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:178719000-178722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:178719000-178723400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:178719200-178722400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:178719200-178737600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:178719400-178721000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:178719600-178721000	Weak transcription	Aorta	Aorta
26	chr3:178719600-178724000	Weak transcription	Left Ventricle	heart
27	chr3:178719600-178733000	Weak transcription	Primary T cells from cord blood	blood
28	chr3:178719800-178720400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:178719800-178721600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:178720000-178721800	Weak transcription	HSMMtube	muscle
31	chr3:178720200-178725000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:178720200-178726400	Weak transcription	Muscle Satellite Cultured Cells	--

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