Variant report

Variant	rs3762688
Chromosome Location	chr3:145924632-145924633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10737947	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.93[ASN][1000 genomes]
rs10804709	0.80[ASN][1000 genomes]
rs10804710	0.93[ASN][1000 genomes]
rs10935611	0.94[CHB][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935613	0.93[ASN][1000 genomes]
rs10935614	0.93[ASN][1000 genomes]
rs10935615	0.93[ASN][1000 genomes]
rs10935616	0.93[ASN][1000 genomes]
rs11709096	0.93[ASN][1000 genomes]
rs11716310	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915448	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.93[ASN][1000 genomes]
rs11919011	0.93[ASN][1000 genomes]
rs12487353	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12633074	0.93[ASN][1000 genomes]
rs1398125	0.82[ASN][1000 genomes]
rs1398529	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512078	0.93[ASN][1000 genomes]
rs1512079	0.93[ASN][1000 genomes]
rs1512080	0.84[ASN][1000 genomes]
rs1512081	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.93[ASN][1000 genomes]
rs1512888	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512890	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1512893	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1606434	0.84[ASN][1000 genomes]
rs1877511	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1913184	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036980	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175544	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.83[MKK][hapmap];0.93[ASN][1000 genomes]
rs2175545	0.93[ASN][1000 genomes]
rs2867081	0.93[ASN][1000 genomes]
rs2867082	0.84[ASN][1000 genomes]
rs2867083	0.93[ASN][1000 genomes]
rs2867084	0.92[ASN][1000 genomes]
rs2903478	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2903479	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs3762686	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804648	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3914252	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273339	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.93[ASN][1000 genomes]
rs4475004	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs4488802	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs4681306	0.93[ASN][1000 genomes]
rs4681307	0.93[ASN][1000 genomes]
rs4681308	0.93[ASN][1000 genomes]
rs6440421	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]
rs6440422	0.93[ASN][1000 genomes]
rs6770057	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[ASN][1000 genomes]
rs6770163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6770278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6775520	0.82[ASN][1000 genomes]
rs6792732	0.93[ASN][1000 genomes]
rs6800307	0.82[ASN][1000 genomes]
rs6805377	0.93[ASN][1000 genomes]
rs7430290	0.93[ASN][1000 genomes]
rs7612683	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621841	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.93[ASN][1000 genomes]
rs7632412	0.93[ASN][1000 genomes]
rs7633252	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7634568	0.93[ASN][1000 genomes]
rs7643778	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.93[ASN][1000 genomes]
rs9756128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809892	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813122	0.93[ASN][1000 genomes]
rs9822280	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825776	0.93[ASN][1000 genomes]
rs9826132	0.93[ASN][1000 genomes]
rs9826360	0.93[ASN][1000 genomes]
rs9826591	0.84[ASN][1000 genomes]
rs9830892	0.84[ASN][1000 genomes]
rs9836419	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]
rs9838801	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9838866	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs9839724	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839874	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845890	0.93[ASN][1000 genomes]
rs9850566	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851511	0.93[ASN][1000 genomes]
rs9855695	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.82[MKK][hapmap];0.93[ASN][1000 genomes]
rs9858823	0.84[ASN][1000 genomes]
rs9859273	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]
rs9863647	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.93[ASN][1000 genomes]
rs9867851	0.93[ASN][1000 genomes]
rs9873891	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs9875799	0.93[ASN][1000 genomes]
rs9877004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3762688	GPR87	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145897000-145933600	Weak transcription	Fetal Stomach	stomach
2	chr3:145903000-145934800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:145905000-145933600	Weak transcription	NHLF	lung
4	chr3:145907000-145938600	Weak transcription	Fetal Intestine Small	intestine
5	chr3:145907600-145939200	Weak transcription	Brain Anterior Caudate	brain
6	chr3:145908200-145936400	Weak transcription	A549	lung
7	chr3:145909600-145939200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:145910400-145932400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:145910400-145940000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:145913800-145939200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:145914200-145937000	Weak transcription	Placenta	Placenta
12	chr3:145914600-145940200	Weak transcription	Gastric	stomach
13	chr3:145914800-145940200	Weak transcription	Psoas Muscle	Psoas
14	chr3:145914800-145940400	Weak transcription	Spleen	Spleen
15	chr3:145917400-145925200	Strong transcription	Adipose Nuclei	Adipose
16	chr3:145917800-145940400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:145918000-145940400	Weak transcription	Pancreas	Pancrea
18	chr3:145918400-145940400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:145918800-145925200	Weak transcription	Fetal Kidney	kidney
20	chr3:145919000-145934800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:145920400-145925800	Strong transcription	Liver	Liver
22	chr3:145920600-145940600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:145921600-145940200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:145922000-145925000	Weak transcription	Colonic Mucosa	Colon
25	chr3:145922000-145925800	Weak transcription	Hela-S3	cervix
26	chr3:145922000-145934800	Weak transcription	Left Ventricle	heart
27	chr3:145922200-145935000	Weak transcription	NHDF-Ad	bronchial
28	chr3:145922400-145925600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:145922600-145925800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:145922600-145933400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:145922600-145940400	Weak transcription	Lung	lung
32	chr3:145923000-145925200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:145923000-145925600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:145923000-145925600	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:145923000-145926000	Strong transcription	HUVEC	blood vessel
36	chr3:145923200-145924800	Strong transcription	Fetal Lung	lung
37	chr3:145923200-145925000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:145923200-145925400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:145923200-145925600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr3:145923200-145926000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr3:145923200-145927600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:145923400-145924800	Strong transcription	Fetal Intestine Large	intestine
43	chr3:145923400-145925600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:145923600-145924800	Strong transcription	HepG2	liver
45	chr3:145923600-145925000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:145923600-145925200	Strong transcription	Ovary	ovary
47	chr3:145924200-145925400	Strong transcription	Primary hematopoietic stem cells	blood
48	chr3:145924400-145939200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:145924400-145944000	Weak transcription	Colon Smooth Muscle	Colon
50	chr3:145924400-145945200	Weak transcription	HSMMtube	muscle

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