Variant report

Variant	rs7687906
Chromosome Location	chr4:86715312-86715313
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10516757	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12710823	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13120732	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17010957	0.93[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs17010961	0.82[AMR][1000 genomes]
rs17011002	0.84[AMR][1000 genomes]
rs2014912	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[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]
rs6531870	0.86[ASW][hapmap];0.91[LWK][hapmap]
rs6829822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72976750	0.82[AMR][1000 genomes]
rs72976751	0.80[AMR][1000 genomes]
rs7671129	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671252	0.86[ASW][hapmap]
rs7687940	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]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv3450999	chr4:86485840-86773745	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv879517	chr4:86677107-86739805	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7687906	THAP9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86701000-86728800	Weak transcription	Right Ventricle	heart
2	chr4:86701200-86715600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:86704000-86715600	Enhancers	Osteobl	bone
4	chr4:86704000-86719800	Enhancers	NHDF-Ad	bronchial
5	chr4:86705800-86719600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:86708400-86718200	Weak transcription	Aorta	Aorta
7	chr4:86709000-86727000	Weak transcription	HSMMtube	muscle
8	chr4:86709200-86727000	Weak transcription	HSMM	muscle
9	chr4:86711000-86719800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:86711200-86715600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:86712400-86718000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:86712800-86715800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:86712800-86719400	Weak transcription	Right Atrium	heart
14	chr4:86713000-86718000	Weak transcription	Left Ventricle	heart
15	chr4:86713200-86717800	Weak transcription	Primary B cells from cord blood	blood
16	chr4:86713200-86717800	Weak transcription	Fetal Muscle Leg	muscle
17	chr4:86713200-86718000	Weak transcription	Fetal Stomach	stomach
18	chr4:86713200-86726400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr4:86713600-86715400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr4:86714400-86716800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:86714600-86715800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:86714600-86718800	Enhancers	HUVEC	blood vessel
23	chr4:86714800-86718000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:86714800-86718000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:86715000-86715400	Weak transcription	NH-A	brain
26	chr4:86715000-86716000	Weak transcription	NHLF	lung
27	chr4:86715200-86717600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:86715200-86718000	Weak transcription	Adipose Nuclei	Adipose
29	chr4:86715200-86719800	Weak transcription	Fetal Lung	lung

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