Variant report

Variant	rs6809153
Chromosome Location	chr3:160071418-160071419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1047210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10513551	0.85[CEU][hapmap]
rs10923	0.82[JPT][hapmap]
rs10936201	0.82[JPT][hapmap]
rs11706810	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11708118	0.82[JPT][hapmap]
rs11709336	0.82[JPT][hapmap]
rs11718121	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11719750	0.82[JPT][hapmap]
rs11720689	0.82[JPT][hapmap]
rs12632030	0.86[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13403	0.85[CEU][hapmap]
rs1451760	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1451761	0.85[CEU][hapmap]
rs1451762	0.85[CEU][hapmap]
rs17236473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17826221	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1873076	0.81[JPT][hapmap]
rs1953506	0.85[CEU][hapmap]
rs1971128	0.82[EUR][1000 genomes]
rs2279457	0.85[CEU][hapmap]
rs2305407	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs3732706	0.92[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs3773372	0.81[CEU][hapmap]
rs3851365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3851366	0.85[CEU][hapmap]
rs4679654	0.80[AMR][1000 genomes]
rs4679881	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs4679885	0.85[CEU][hapmap]
rs4679890	0.80[CEU][hapmap]
rs4679891	0.80[CEU][hapmap]
rs4680576	0.85[CEU][hapmap]
rs4680579	0.85[CEU][hapmap]
rs4680580	0.85[CEU][hapmap]
rs4680585	0.85[CEU][hapmap]
rs4680588	0.85[CEU][hapmap]
rs4680589	0.81[EUR][1000 genomes]
rs4680591	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55992947	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56156703	0.80[EUR][1000 genomes]
rs6441313	0.85[CEU][hapmap]
rs6441314	0.85[CEU][hapmap]
rs6441319	0.81[CEU][hapmap]
rs6441320	0.85[CEU][hapmap]
rs6785881	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6790951	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6791056	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6791261	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs6793560	0.88[CEU][hapmap]
rs6798183	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];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798668	0.81[CEU][hapmap]
rs6803828	0.85[CEU][hapmap]
rs7355951	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7611130	0.85[CEU][hapmap]
rs7620828	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7624902	0.85[CEU][hapmap]
rs7627555	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];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7627756	0.81[CEU][hapmap]
rs7629	0.85[CEU][hapmap]
rs7631792	0.85[CEU][hapmap]
rs7634108	0.84[CEU][hapmap]
rs7634826	0.85[CEU][hapmap]
rs7640072	0.81[CEU][hapmap]
rs7647873	0.81[CEU][hapmap]
rs869467	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869468	0.85[CEU][hapmap]
rs9968151	0.85[CEU][hapmap]

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	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
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6809153	IFT80	cis	parietal	SCAN
rs6809153	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159977800-160073000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:160025400-160073000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:160025600-160072000	Weak transcription	Thymus	Thymus
4	chr3:160025600-160073200	Weak transcription	Left Ventricle	heart
5	chr3:160034800-160082800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:160049400-160090600	Weak transcription	NH-A	brain
7	chr3:160049800-160073200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:160054400-160091600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:160055200-160103400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:160055800-160072800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:160055800-160087800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:160056200-160075200	Weak transcription	HSMM	muscle
13	chr3:160056200-160091000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:160056400-160072000	Weak transcription	Brain Anterior Caudate	brain
15	chr3:160056400-160073000	Weak transcription	Fetal Stomach	stomach
16	chr3:160056400-160082800	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:160056400-160098000	Weak transcription	Aorta	Aorta
18	chr3:160056600-160072000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:160056600-160072000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:160056600-160072600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:160056600-160073200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:160056600-160082400	Weak transcription	Fetal Lung	lung
23	chr3:160056600-160082800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:160056600-160083200	Weak transcription	Fetal Intestine Small	intestine
25	chr3:160056600-160091600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:160057200-160072800	Weak transcription	Primary B cells from cord blood	blood
27	chr3:160057600-160072800	Weak transcription	Fetal Intestine Large	intestine
28	chr3:160058400-160088800	Weak transcription	Osteobl	bone
29	chr3:160058600-160073200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:160058800-160083200	Weak transcription	GM12878-XiMat	blood
31	chr3:160059000-160072200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:160059000-160072800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:160059400-160077200	Weak transcription	Lung	lung
34	chr3:160061000-160071800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:160061000-160071800	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:160061400-160109600	Weak transcription	Fetal Heart	heart
37	chr3:160062000-160072800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:160062200-160072000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:160062400-160072800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:160062800-160073400	Weak transcription	A549	lung
41	chr3:160063000-160074400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:160063200-160072000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:160063400-160073600	Weak transcription	Pancreas	Pancrea
44	chr3:160063400-160094000	Weak transcription	Fetal Brain Female	brain
45	chr3:160064400-160077800	Weak transcription	Spleen	Spleen
46	chr3:160065000-160072800	Weak transcription	Ovary	ovary
47	chr3:160065000-160082800	Weak transcription	NHDF-Ad	bronchial
48	chr3:160065000-160091600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:160065200-160073200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:160065400-160072400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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