Variant report

Variant	rs6440421
Chromosome Location	chr3:145946816-145946817
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	chr3:145944002..145945741-chr3:145946348..145947988,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10737947	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];0.95[ASN][1000 genomes]
rs10804709	0.81[ASN][1000 genomes]
rs10804710	0.95[ASN][1000 genomes]
rs10935611	0.94[CHB][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935613	0.95[ASN][1000 genomes]
rs10935614	0.95[ASN][1000 genomes]
rs10935615	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10935616	0.95[ASN][1000 genomes]
rs11709096	0.95[ASN][1000 genomes]
rs11716310	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11915448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11919011	0.95[ASN][1000 genomes]
rs12487353	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12633074	0.94[ASN][1000 genomes]
rs1398125	0.83[ASN][1000 genomes]
rs1398529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512078	0.95[ASN][1000 genomes]
rs1512079	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1512080	0.86[ASN][1000 genomes]
rs1512081	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];0.94[ASN][1000 genomes]
rs1512888	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512890	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1512893	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1606434	0.86[ASN][1000 genomes]
rs1877511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1913184	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2036980	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2175544	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.94[ASN][1000 genomes]
rs2175545	0.94[ASN][1000 genomes]
rs2867081	0.95[ASN][1000 genomes]
rs2867082	0.86[ASN][1000 genomes]
rs2867083	0.95[ASN][1000 genomes]
rs2867084	0.93[ASN][1000 genomes]
rs2903478	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2903479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3762686	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3804648	0.81[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3804654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3914252	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4273339	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4475004	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4488802	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];0.95[ASN][1000 genomes]
rs4681306	0.95[ASN][1000 genomes]
rs4681307	0.94[ASN][1000 genomes]
rs4681308	0.94[ASN][1000 genomes]
rs6440422	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6770057	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs6770163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775520	0.83[ASN][1000 genomes]
rs6792732	0.94[ASN][1000 genomes]
rs6800307	0.83[ASN][1000 genomes]
rs6805377	0.94[ASN][1000 genomes]
rs7430290	0.94[ASN][1000 genomes]
rs7612683	0.91[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7621841	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];0.95[ASN][1000 genomes]
rs7632412	0.94[ASN][1000 genomes]
rs7633252	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7634568	0.94[ASN][1000 genomes]
rs7643778	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];0.95[ASN][1000 genomes]
rs9756128	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9809892	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9813122	0.95[ASN][1000 genomes]
rs9822280	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9825776	0.95[ASN][1000 genomes]
rs9826132	0.95[ASN][1000 genomes]
rs9826360	0.95[ASN][1000 genomes]
rs9826591	0.86[ASN][1000 genomes]
rs9830892	0.86[ASN][1000 genomes]
rs9836419	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs9838801	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838866	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs9839724	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9839874	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9845890	0.95[ASN][1000 genomes]
rs9850566	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9851511	0.95[ASN][1000 genomes]
rs9855695	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];0.94[ASN][1000 genomes]
rs9858823	0.86[ASN][1000 genomes]
rs9859273	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs9863647	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];0.94[ASN][1000 genomes]
rs9867851	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9873891	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9875799	0.94[ASN][1000 genomes]
rs9877004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012485	chr3:145861750-145947125	Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536758	chr3:145861750-145947125	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv877614	chr3:145903426-146025896	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv877615	chr3:145910430-145988231	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv877616	chr3:145921954-145983688	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3333601	chr3:145940702-146068210	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv3416330	chr3:145941029-146068457	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6440421	GPR87	cis	parietal	SCAN
rs6440421	PLSCR4	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145925400-145952800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:145925600-145950800	Weak transcription	Fetal Kidney	kidney
3	chr3:145934600-145952200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:145940600-145953000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:145940600-145953600	Weak transcription	NHDF-Ad	bronchial
6	chr3:145941400-145948400	Weak transcription	Osteobl	bone
7	chr3:145941600-145947000	Weak transcription	Right Atrium	heart
8	chr3:145941600-145952200	Weak transcription	Left Ventricle	heart
9	chr3:145941600-145952600	Weak transcription	Fetal Intestine Small	intestine
10	chr3:145941600-145954000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:145942000-145947000	Weak transcription	Fetal Intestine Large	intestine
12	chr3:145942200-145953400	Weak transcription	HUVEC	blood vessel
13	chr3:145944800-145947200	Enhancers	Adipose Nuclei	Adipose
14	chr3:145944800-145947400	Enhancers	Liver	Liver
15	chr3:145945200-145959800	Weak transcription	Ovary	ovary
16	chr3:145945400-145948200	Weak transcription	Aorta	Aorta
17	chr3:145945600-145947000	Weak transcription	Pancreas	Pancrea
18	chr3:145946000-145947200	Enhancers	Colon Smooth Muscle	Colon
19	chr3:145946000-145952400	Weak transcription	Fetal Stomach	stomach
20	chr3:145946200-145952600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:145946400-145947800	Weak transcription	Fetal Lung	lung
22	chr3:145946400-145953000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:145946800-145947400	Enhancers	Rectal Mucosa Donor 31	rectum

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