Variant report

Variant	rs7624902
Chromosome Location	chr3:160004026-160004027
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10212236	0.80[ASN][1000 genomes]
rs1047210	0.85[CEU][hapmap]
rs10513551	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10936199	0.86[YRI][hapmap]
rs11706810	0.85[CEU][hapmap]
rs11918749	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13403	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1451761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1451762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236473	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs17826221	0.85[CEU][hapmap]
rs1953506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2152425	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279457	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2305407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851365	0.85[CEU][hapmap]
rs3851366	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap]
rs4091703	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs41272947	0.94[ASN][1000 genomes]
rs4679879	0.85[YRI][hapmap]
rs4679880	0.89[YRI][hapmap]
rs4679881	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679885	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4679889	0.80[ASN][1000 genomes]
rs4680576	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680585	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4680587	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4680588	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55687857	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55731730	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56394279	0.81[AMR][1000 genomes]
rs58322641	0.80[ASN][1000 genomes]
rs58665246	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60009222	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60460891	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62272186	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6441319	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.96[ASN][1000 genomes]
rs6441320	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs6778728	0.89[YRI][hapmap]
rs6791261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792612	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6793560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6798183	0.85[CEU][hapmap]
rs6798668	0.96[CEU][hapmap]
rs6803828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6808083	0.94[CHB][hapmap];0.83[AMR][1000 genomes]
rs6809153	0.85[CEU][hapmap]
rs6809313	0.85[CEU][hapmap]
rs721023	0.80[ASN][1000 genomes]
rs73154592	0.95[ASN][1000 genomes]
rs7356111	0.98[ASN][1000 genomes]
rs7611130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7620828	0.84[CEU][hapmap]
rs7627555	0.85[CEU][hapmap]
rs7627749	0.80[ASN][1000 genomes]
rs7627756	0.80[ASN][1000 genomes]
rs7629	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7629202	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7631792	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7634108	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7634826	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs869468	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9798898	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9799314	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9968151	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7624902	IFT80	cis	parietal	SCAN
rs7624902	EGFL6	trans	lymphoblastoid	seeQTL
rs7624902	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159971400-160035800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:159971800-160009600	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:159972600-160009400	Weak transcription	Fetal Stomach	stomach
4	chr3:159974200-160038000	Weak transcription	Fetal Brain Male	brain
5	chr3:159974800-160014400	Weak transcription	HSMM	muscle
6	chr3:159975000-160025600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:159975000-160028000	Weak transcription	Brain Anterior Caudate	brain
8	chr3:159975000-160034200	Weak transcription	Fetal Intestine Large	intestine
9	chr3:159975200-160036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:159975600-160009600	Weak transcription	Fetal Intestine Small	intestine
11	chr3:159975600-160046600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:159976200-160039000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:159977800-160014400	Weak transcription	NHDF-Ad	bronchial
14	chr3:159977800-160073000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:159979000-160007800	Weak transcription	Liver	Liver
16	chr3:159981200-160038200	Weak transcription	Esophagus	oesophagus
17	chr3:159983000-160009400	Weak transcription	Pancreas	Pancrea
18	chr3:159983400-160009400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:159983400-160014200	Weak transcription	HSMMtube	muscle
20	chr3:159983600-160020400	Weak transcription	Brain Germinal Matrix	brain
21	chr3:159984600-160014600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:159984800-160038200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:159985800-160011600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:159986000-160009200	Weak transcription	Thymus	Thymus
25	chr3:159986000-160009400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:159986400-160009600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:159986400-160024800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr3:159987000-160014400	Weak transcription	NHLF	lung
29	chr3:159988200-160030200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:159988800-160004800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:159989400-160005200	Weak transcription	Adipose Nuclei	Adipose
32	chr3:159990200-160005400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr3:159991000-160009400	Weak transcription	Gastric	stomach
34	chr3:159991000-160024800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:159992200-160008400	Weak transcription	HepG2	liver
36	chr3:159992400-160014000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:159992400-160035400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:159992600-160022600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:159992800-160007400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:159992800-160014400	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:159992800-160026400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr3:159992800-160033400	Weak transcription	Fetal Kidney	kidney
43	chr3:159992800-160036400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:159992800-160036600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:159993000-160019600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:159993200-160005200	Weak transcription	Fetal Brain Female	brain
47	chr3:159993600-160016800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:159994600-160025000	Weak transcription	Dnd41	blood
49	chr3:159994800-160009800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:159995000-160014200	Weak transcription	Osteobl	bone

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