Variant report

Variant	rs4577503
Chromosome Location	chr3:99657922-99657923
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10936003	0.80[AFR][1000 genomes]
rs10936008	0.82[TSI][hapmap]
rs11719468	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12488245	0.96[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap]
rs1287284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13059754	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1384062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387647	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap]
rs1610509	0.88[JPT][hapmap]
rs16841874	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap]
rs1718235	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.85[ASN][1000 genomes]
rs2638948	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35422475	0.85[AMR][1000 genomes]
rs4928150	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928151	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4928153	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap]
rs4928230	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.84[ASN][1000 genomes]
rs4928235	0.87[AMR][1000 genomes]
rs4928237	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs58704213	0.81[ASN][1000 genomes]
rs6440967	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs6802817	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap]
rs6806323	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs704571	0.88[JPT][hapmap]
rs704572	0.92[JPT][hapmap]
rs704574	0.88[JPT][hapmap]
rs7613864	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638900	0.82[TSI][hapmap]
rs7649349	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs7650727	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs766778	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs792831	0.88[JPT][hapmap]
rs792835	0.88[JPT][hapmap]
rs792836	0.88[JPT][hapmap]
rs792837	0.88[JPT][hapmap]
rs793437	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793439	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.85[ASN][1000 genomes]
rs793440	0.82[TSI][hapmap]
rs793443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793446	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793456	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793464	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];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793470	0.82[TSI][hapmap]
rs793474	0.82[TSI][hapmap]
rs793475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793476	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793483	0.88[JPT][hapmap]
rs793485	0.88[JPT][hapmap]
rs793497	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs793502	0.83[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.85[ASN][1000 genomes]
rs793503	0.82[TSI][hapmap]
rs796976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796978	0.82[TSI][hapmap]
rs813218	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.85[ASN][1000 genomes]
rs902159	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs923472	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9811920	0.92[CEU][hapmap];0.85[GIH][hapmap];0.83[LWK][hapmap]
rs9837131	0.92[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap]

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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4577503	OR5H6	cis	cerebellum	SCAN
rs4577503	C3orf26	Cis_1M	lymphoblastoid	RTeQTL
rs4577503	SENP7	cis	parietal	SCAN
rs4577503	EPHX1	trans	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99644800-99663200	Weak transcription	Esophagus	oesophagus
2	chr3:99648800-99663200	Weak transcription	Gastric	stomach
3	chr3:99648800-99664000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:99649600-99662800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:99650400-99663000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:99650400-99667400	Weak transcription	A549	lung
7	chr3:99650600-99662800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:99650600-99663200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:99654000-99663000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:99654600-99658000	Weak transcription	Left Ventricle	heart
11	chr3:99654600-99659400	Weak transcription	Right Atrium	heart
12	chr3:99654600-99664000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:99654800-99663000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:99654800-99663000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:99654800-99663000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:99654800-99663200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:99655200-99663000	Weak transcription	Brain Anterior Caudate	brain
18	chr3:99656000-99658800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:99656200-99658200	Flanking Active TSS	GM12878-XiMat	blood
20	chr3:99656200-99658200	Enhancers	Osteobl	bone
21	chr3:99656200-99658400	Enhancers	Muscle Satellite Cultured Cells	--
22	chr3:99656200-99658400	Enhancers	HSMM	muscle
23	chr3:99656200-99658600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr3:99656200-99659400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:99656200-99659800	Enhancers	Rectal Smooth Muscle	rectum
26	chr3:99656200-99660600	Enhancers	Stomach Mucosa	stomach
27	chr3:99656400-99658000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:99656400-99658000	Enhancers	Fetal Intestine Large	intestine
29	chr3:99656400-99658200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:99656400-99658200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr3:99656400-99658200	Enhancers	NHLF	lung
32	chr3:99656400-99658400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:99656400-99658400	Enhancers	Small Intestine	intestine
34	chr3:99656400-99658600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr3:99656400-99659200	Enhancers	Fetal Intestine Small	intestine
36	chr3:99656400-99659600	Enhancers	Fetal Stomach	stomach
37	chr3:99656400-99660000	Enhancers	Colon Smooth Muscle	Colon
38	chr3:99656600-99658000	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr3:99656600-99659000	Enhancers	Fetal Lung	lung
40	chr3:99656600-99662800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:99656800-99659800	Enhancers	Stomach Smooth Muscle	stomach
42	chr3:99657000-99658000	Weak transcription	Ovary	ovary
43	chr3:99657200-99658800	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr3:99657200-99659000	Weak transcription	Aorta	Aorta
45	chr3:99657200-99662600	Weak transcription	Brain Angular Gyrus	brain
46	chr3:99657400-99658000	Weak transcription	Psoas Muscle	Psoas
47	chr3:99657400-99658400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:99657400-99663000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:99657400-99663200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:99657600-99658000	Weak transcription	Right Ventricle	heart

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