Variant report

Variant	rs6798183
Chromosome Location	chr3:160074767-160074768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1047210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[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];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11708118	0.82[JPT][hapmap]
rs11709336	0.82[JPT][hapmap]
rs11718121	0.89[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];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13403	0.85[CEU][hapmap]
rs1451760	0.95[AMR][1000 genomes];0.96[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];0.87[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];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1873076	0.81[JPT][hapmap]
rs1953506	0.85[CEU][hapmap]
rs1971128	0.81[EUR][1000 genomes]
rs2279457	0.85[CEU][hapmap]
rs2305407	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs3732706	0.92[CEU][hapmap];0.92[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];0.84[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3851366	0.85[CEU][hapmap]
rs4679881	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs4679885	0.85[CEU][hapmap]
rs4679890	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	0.80[EUR][1000 genomes]
rs4680591	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55992947	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441313	0.85[CEU][hapmap]
rs6441314	0.85[CEU][hapmap]
rs6441319	0.81[CEU][hapmap]
rs6441320	0.85[CEU][hapmap]
rs6785881	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6790951	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6791056	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6791261	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs6793560	0.88[CEU][hapmap]
rs6798668	0.81[CEU][hapmap]
rs6803828	0.85[CEU][hapmap]
rs6809153	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]
rs7355951	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[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];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.97[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];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[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	0.80[CEU][hapmap]
rs7647873	0.81[CEU][hapmap]
rs869467	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[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
rs6798183	IFT80	cis	parietal	SCAN
rs6798183	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160034800-160082800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:160049400-160090600	Weak transcription	NH-A	brain
3	chr3:160054400-160091600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:160055200-160103400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:160055800-160087800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:160056200-160075200	Weak transcription	HSMM	muscle
7	chr3:160056200-160091000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:160056400-160082800	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:160056400-160098000	Weak transcription	Aorta	Aorta
10	chr3:160056600-160082400	Weak transcription	Fetal Lung	lung
11	chr3:160056600-160082800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:160056600-160083200	Weak transcription	Fetal Intestine Small	intestine
13	chr3:160056600-160091600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:160058400-160088800	Weak transcription	Osteobl	bone
15	chr3:160058800-160083200	Weak transcription	GM12878-XiMat	blood
16	chr3:160059400-160077200	Weak transcription	Lung	lung
17	chr3:160061400-160109600	Weak transcription	Fetal Heart	heart
18	chr3:160063400-160094000	Weak transcription	Fetal Brain Female	brain
19	chr3:160064400-160077800	Weak transcription	Spleen	Spleen
20	chr3:160065000-160082800	Weak transcription	NHDF-Ad	bronchial
21	chr3:160065000-160091600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:160066200-160086000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:160066400-160099200	Weak transcription	NHEK	skin
24	chr3:160066800-160083200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:160067800-160097800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:160068600-160086000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:160068600-160096000	Weak transcription	Gastric	stomach
28	chr3:160068800-160094000	Weak transcription	Adipose Nuclei	Adipose
29	chr3:160068800-160094000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:160069000-160115200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:160069800-160087600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:160070200-160077400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:160070200-160086200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:160070400-160092400	Weak transcription	HMEC	breast
35	chr3:160070600-160078000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:160070600-160085800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:160071000-160091000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:160071200-160075200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:160071400-160083200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:160071400-160098200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:160071400-160102000	Weak transcription	Small Intestine	intestine
42	chr3:160071600-160075400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr3:160071600-160099400	Weak transcription	Placenta	Placenta
44	chr3:160071800-160091800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:160071800-160092000	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr3:160072000-160075200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:160072000-160075600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:160072000-160077200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr3:160072000-160096400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:160072400-160075200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links