Variant report

Variant	rs9862595
Chromosome Location	chr3:160279879-160279880
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:160275859-160280661	HepG2	liver:	n/a	n/a
2	KAP1	chr3:160279706-160280163	K562	blood:	n/a	n/a
3	POLR2A	chr3:160279717-160280495	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:160279142-160279898	A549	lung:	n/a	n/a
5	POLR2A	chr3:160279108-160285420	IMR90	lung:	n/a	n/a
6	POLR2A	chr3:160279829-160280081	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160166040..160169765-chr3:160279150..160282681,5	K562	blood:

Variant related genes	Relation type
KRT8P12	TF binding region
ENSG00000213186	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10212236	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10513551	0.83[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs1317365	0.88[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13403	0.83[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs1451761	0.81[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs1451762	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1451764	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1551190	1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1584688	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17236473	0.84[JPT][hapmap]
rs17236544	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17570467	0.96[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1882126	0.96[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1882127	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920642	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1920662	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1920664	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279457	0.92[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[ASN][1000 genomes]
rs2305407	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2366969	0.85[ASN][1000 genomes]
rs28705750	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2886825	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732707	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3773372	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3851366	0.92[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap]
rs4091703	0.89[ASN][1000 genomes]
rs4292273	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4292274	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4621370	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4679655	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4679885	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[ASN][1000 genomes]
rs4679888	0.83[EUR][1000 genomes]
rs4679889	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4679890	0.96[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4679891	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4679896	0.85[EUR][1000 genomes]
rs4679899	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4679900	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4680579	0.83[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs4680580	0.83[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs4680585	0.83[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[ASN][1000 genomes]
rs4680587	0.89[ASN][1000 genomes]
rs4680588	0.83[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs56197102	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58322641	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60460891	0.86[ASN][1000 genomes]
rs62272791	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62272792	0.86[EUR][1000 genomes]
rs62272794	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62272800	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62272810	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441319	1.00[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap]
rs6441320	0.92[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[ASN][1000 genomes]
rs6441324	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6768975	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6793560	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6798668	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs6801300	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6806505	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6808083	0.82[CHB][hapmap]
rs721022	0.82[ASW][hapmap];0.88[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs721023	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];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7611130	0.83[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs7618974	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7621724	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7627749	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7627756	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7629	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[ASN][1000 genomes]
rs7629202	0.84[ASN][1000 genomes]
rs7629423	0.80[JPT][hapmap]
rs7631792	0.92[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.80[ASN][1000 genomes]
rs7634108	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7634826	0.92[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.88[MEX][hapmap]
rs7640072	0.96[CEU][hapmap];0.94[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7643779	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7644453	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7645832	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7647873	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9968151	0.92[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	nsv877701	chr3:160228001-160283815	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
6	nsv877702	chr3:160262803-160304614	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9862595	IFT80	cis	parietal	SCAN
rs9862595	BCHE	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160234600-160281000	Weak transcription	Aorta	Aorta
2	chr3:160240200-160280400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:160247000-160281000	Weak transcription	Thymus	Thymus
4	chr3:160251200-160282000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:160261800-160281000	Weak transcription	Ovary	ovary
6	chr3:160264200-160282000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:160268400-160281000	Weak transcription	Fetal Thymus	thymus
8	chr3:160268400-160281600	Weak transcription	Fetal Stomach	stomach
9	chr3:160269200-160281000	Weak transcription	Fetal Intestine Large	intestine
10	chr3:160269400-160281600	Weak transcription	Fetal Kidney	kidney
11	chr3:160269400-160281600	Weak transcription	Fetal Lung	lung
12	chr3:160270000-160281800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:160270200-160282000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:160270400-160280800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:160271400-160281000	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:160272600-160280000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:160272600-160281000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:160272800-160280200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:160273000-160280800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:160273000-160281000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:160273000-160281000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:160273000-160281000	Weak transcription	Fetal Intestine Small	intestine
23	chr3:160273000-160281000	Weak transcription	Right Ventricle	heart
24	chr3:160273000-160281600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:160273400-160281000	Weak transcription	Brain Germinal Matrix	brain
26	chr3:160274200-160282000	Weak transcription	Gastric	stomach
27	chr3:160276000-160281800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:160276800-160281600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr3:160276800-160281600	Enhancers	Liver	Liver
30	chr3:160276800-160281800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:160276800-160281800	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr3:160277000-160281000	Enhancers	Colon Smooth Muscle	Colon
33	chr3:160277200-160281200	Enhancers	Rectal Smooth Muscle	rectum
34	chr3:160277200-160282000	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr3:160277400-160280200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:160277400-160280200	Enhancers	Adipose Nuclei	Adipose
37	chr3:160277400-160280800	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr3:160277400-160281000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:160277400-160281800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr3:160277600-160280800	Enhancers	HepG2	liver
41	chr3:160277600-160281800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:160277800-160280200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:160278000-160281000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:160278000-160281800	Enhancers	Primary B cells from cord blood	blood
45	chr3:160278400-160281600	Enhancers	Fetal Heart	heart
46	chr3:160278600-160280600	Weak transcription	Brain Anterior Caudate	brain
47	chr3:160278600-160280800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:160278600-160281000	Weak transcription	HSMMtube	muscle
49	chr3:160279000-160280200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:160279000-160280400	Enhancers	Pancreatic Islets	Pancreatic Islet

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