Variant report

Variant	rs6809313
Chromosome Location	chr3:160065568-160065569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10513551	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs13403	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs1451761	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs1451762	0.85[CEU][hapmap]
rs1451763	0.84[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs1953506	0.84[CEU][hapmap]
rs2152425	0.80[CEU][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2279457	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs2305407	0.91[CEU][hapmap]
rs3773372	0.81[CEU][hapmap];0.80[GIH][hapmap]
rs3851364	0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs3851366	0.85[CEU][hapmap]
rs41272947	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4679881	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs4679885	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs4679890	0.84[CEU][hapmap]
rs4679891	0.80[CEU][hapmap]
rs4680576	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs4680579	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs4680580	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs4680585	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs4680588	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs6441313	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs6441314	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs6441315	0.91[ASN][1000 genomes]
rs6441319	0.88[CEU][hapmap];0.84[CHB][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs6441320	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs6789211	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6791261	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs6793560	0.84[CEU][hapmap]
rs6798668	0.84[CEU][hapmap]
rs6803828	0.85[CEU][hapmap]
rs721022	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs721023	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs7356111	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7611130	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs7624902	0.85[CEU][hapmap]
rs7627756	0.88[CEU][hapmap];0.83[GIH][hapmap]
rs7629	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs7631792	0.85[CEU][hapmap];0.87[GIH][hapmap]
rs7632307	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7634108	0.88[CEU][hapmap]
rs7634826	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs7640072	0.81[CEU][hapmap]
rs7647873	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs869468	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs9830588	0.89[YRI][hapmap]
rs9834276	0.81[YRI][hapmap]
rs9872543	0.90[YRI][hapmap]
rs9968151	0.85[CEU][hapmap];0.85[GIH][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
rs6809313	IFT80	cis	parietal	SCAN
rs6809313	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 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	chr3:160037000-160070200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:160049400-160090600	Weak transcription	NH-A	brain
8	chr3:160049800-160073200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:160054400-160091600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:160055200-160103400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:160055800-160072800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:160055800-160087800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:160056000-160070600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:160056200-160075200	Weak transcription	HSMM	muscle
15	chr3:160056200-160091000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:160056400-160070200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:160056400-160072000	Weak transcription	Brain Anterior Caudate	brain
18	chr3:160056400-160073000	Weak transcription	Fetal Stomach	stomach
19	chr3:160056400-160082800	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:160056400-160098000	Weak transcription	Aorta	Aorta
21	chr3:160056600-160072000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:160056600-160072000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:160056600-160072600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:160056600-160073200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:160056600-160082400	Weak transcription	Fetal Lung	lung
26	chr3:160056600-160082800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:160056600-160083200	Weak transcription	Fetal Intestine Small	intestine
28	chr3:160056600-160091600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:160057000-160070400	Weak transcription	Fetal Thymus	thymus
30	chr3:160057200-160072800	Weak transcription	Primary B cells from cord blood	blood
31	chr3:160057600-160072800	Weak transcription	Fetal Intestine Large	intestine
32	chr3:160058400-160088800	Weak transcription	Osteobl	bone
33	chr3:160058600-160073200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:160058800-160083200	Weak transcription	GM12878-XiMat	blood
35	chr3:160059000-160072200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr3:160059000-160072800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:160059400-160077200	Weak transcription	Lung	lung
38	chr3:160061000-160071800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:160061000-160071800	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:160061400-160109600	Weak transcription	Fetal Heart	heart
41	chr3:160062000-160072800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:160062200-160072000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:160062400-160072800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:160062800-160073400	Weak transcription	A549	lung
45	chr3:160063000-160074400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:160063200-160072000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:160063400-160073600	Weak transcription	Pancreas	Pancrea
48	chr3:160063400-160094000	Weak transcription	Fetal Brain Female	brain
49	chr3:160064400-160067800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:160064400-160077800	Weak transcription	Spleen	Spleen

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