Variant report

Variant	rs3732706
Chromosome Location	chr3:160214469-160214470
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160116809..160118818-chr3:160213302..160214822,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM59-1	chr3:160212796-160215639	NONHSAT092996

Variant related genes	Relation type
ENSG00000113810	Chromatin interaction
ENSG00000068885	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1047210	0.92[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10923	0.89[ASW][hapmap];0.84[YRI][hapmap]
rs10936201	0.88[ASW][hapmap];0.84[YRI][hapmap]
rs10936203	0.89[ASW][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs11706810	0.92[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11709232	0.84[YRI][hapmap]
rs11718121	0.81[EUR][1000 genomes]
rs11720689	0.89[ASW][hapmap];0.84[YRI][hapmap]
rs12152435	0.81[AFR][1000 genomes]
rs12630956	0.83[AFR][1000 genomes]
rs12632030	0.81[EUR][1000 genomes]
rs12638633	0.81[AFR][1000 genomes]
rs12639488	0.91[YRI][hapmap]
rs1369666	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1451760	0.82[EUR][1000 genomes]
rs17236473	0.92[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17236544	0.82[CEU][hapmap];0.80[GIH][hapmap]
rs17570467	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs17826221	0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17826257	0.81[JPT][hapmap]
rs1873076	1.00[ASW][hapmap];0.84[YRI][hapmap]
rs1882126	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs1882127	0.82[CEU][hapmap]
rs1920642	0.82[CEU][hapmap]
rs1920664	0.82[CEU][hapmap]
rs1953506	0.82[CEU][hapmap]
rs1971128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2123003	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3773372	0.82[CEU][hapmap]
rs3851365	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851366	0.82[GIH][hapmap];0.88[JPT][hapmap]
rs4679654	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4679888	0.80[ASN][1000 genomes]
rs4679890	0.81[CEU][hapmap]
rs4679891	0.81[CEU][hapmap]
rs4679895	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679899	0.82[CEU][hapmap]
rs4680589	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680591	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55992947	0.81[EUR][1000 genomes]
rs56156703	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6441324	0.82[CEU][hapmap]
rs6768975	0.82[CEU][hapmap]
rs6785881	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6793560	0.81[CEU][hapmap]
rs6798183	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]
rs6798668	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs6808083	0.88[JPT][hapmap]
rs6809153	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]
rs73875285	0.86[AFR][1000 genomes]
rs73875290	0.81[AFR][1000 genomes]
rs7618974	0.82[CEU][hapmap]
rs7620828	0.92[CEU][hapmap];0.92[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs7621724	0.82[CEU][hapmap]
rs7627555	0.92[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs7627756	0.82[CEU][hapmap]
rs7634826	0.88[JPT][hapmap]
rs7640072	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs7643779	0.82[CEU][hapmap]
rs7647873	0.82[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	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
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3732706	IFT80	cis	parietal	SCAN
rs3732706	SMC4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160204000-160215800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr3:160204000-160216000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:160204000-160219000	Weak transcription	Lung	lung
4	chr3:160204000-160219000	Weak transcription	Thymus	Thymus
5	chr3:160204000-160224000	Weak transcription	Gastric	stomach
6	chr3:160204000-160238200	Weak transcription	Small Intestine	intestine
7	chr3:160204200-160215600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:160204200-160215800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:160204200-160215800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr3:160204200-160215800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:160204200-160215800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:160204200-160215800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:160204200-160215800	Weak transcription	Fetal Thymus	thymus
14	chr3:160204200-160215800	Weak transcription	HSMM	muscle
15	chr3:160204200-160215800	Weak transcription	NHDF-Ad	bronchial
16	chr3:160204200-160216000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:160204200-160216000	Weak transcription	Osteobl	bone
18	chr3:160204200-160216200	Weak transcription	Primary T cells from cord blood	blood
19	chr3:160204200-160216200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:160204200-160216200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:160204200-160216200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:160204200-160216200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:160204200-160216200	Weak transcription	Liver	Liver
24	chr3:160204200-160216200	Weak transcription	HMEC	breast
25	chr3:160204200-160216400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:160204200-160216400	Weak transcription	HUVEC	blood vessel
27	chr3:160204200-160216800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:160204200-160217200	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:160204200-160217600	Weak transcription	NH-A	brain
30	chr3:160204200-160218800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:160204200-160218800	Weak transcription	Fetal Intestine Large	intestine
32	chr3:160204200-160219000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:160204200-160219000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:160204200-160219000	Weak transcription	NHEK	skin
35	chr3:160204200-160219200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:160204200-160219200	Weak transcription	Aorta	Aorta
37	chr3:160204200-160219200	Weak transcription	Left Ventricle	heart
38	chr3:160204200-160219400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:160204200-160224400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:160204200-160224800	Weak transcription	GM12878-XiMat	blood
41	chr3:160204200-160225400	Weak transcription	Fetal Kidney	kidney
42	chr3:160204400-160215600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:160204400-160215800	Weak transcription	Primary B cells from cord blood	blood
44	chr3:160204400-160216400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:160209200-160218600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:160209200-160219200	Weak transcription	Fetal Stomach	stomach
47	chr3:160209800-160218600	Weak transcription	HSMMtube	muscle
48	chr3:160210200-160218400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:160210200-160219000	Weak transcription	Brain Anterior Caudate	brain
50	chr3:160210600-160216000	Weak transcription	Primary monocytes fromperipheralblood	blood

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