Variant report

Variant	rs4679894
Chromosome Location	chr3:160279411-160279412
allele	A/G
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	POLR2A	chr3:160279142-160279898	A549	lung:	n/a	n/a
3	POLR2A	chr3:160279108-160285420	IMR90	lung:	n/a	n/a
4	STAT3	chr3:160279285-160279423	MCF10A-Er-Src	breast:	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: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1141023	0.94[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236389	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236452	0.94[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236487	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs17826161	0.94[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1882124	0.87[ASN][1000 genomes]
rs1882128	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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920645	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1920648	0.87[ASN][1000 genomes]
rs1920654	0.87[ASN][1000 genomes]
rs1979160	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2029361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35281166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41272955	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41272957	0.96[ASN][1000 genomes]
rs4254702	0.88[CEU][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4434183	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679883	0.94[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679887	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680577	0.96[ASN][1000 genomes]
rs4680582	0.88[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap];0.96[ASN][1000 genomes]
rs4680590	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];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55853078	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56051094	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56322040	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6776582	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780828	0.87[ASN][1000 genomes]
rs6806971	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154567	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73154591	0.96[ASN][1000 genomes]
rs73154596	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154600	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154602	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155903	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155920	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155922	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155924	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622031	0.96[ASN][1000 genomes]
rs9826290	0.96[ASN][1000 genomes]
rs9845172	0.87[ASN][1000 genomes]
rs9847144	0.87[ASN][1000 genomes]
rs9876980	0.87[ASN][1000 genomes]

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	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
5	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
6	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
7	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

No data

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	chr3:160254000-160279800	Weak transcription	Placenta	Placenta
6	chr3:160260200-160279600	Weak transcription	Osteobl	bone
7	chr3:160261800-160281000	Weak transcription	Ovary	ovary
8	chr3:160264200-160282000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:160268400-160281000	Weak transcription	Fetal Thymus	thymus
10	chr3:160268400-160281600	Weak transcription	Fetal Stomach	stomach
11	chr3:160268800-160279800	Weak transcription	NHDF-Ad	bronchial
12	chr3:160269200-160281000	Weak transcription	Fetal Intestine Large	intestine
13	chr3:160269400-160281600	Weak transcription	Fetal Kidney	kidney
14	chr3:160269400-160281600	Weak transcription	Fetal Lung	lung
15	chr3:160269800-160279600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:160270000-160281800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:160270200-160282000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:160270400-160280800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:160271400-160281000	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:160272400-160279800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:160272600-160280000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:160272600-160281000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:160272800-160279600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:160272800-160280200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:160273000-160279600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:160273000-160279600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:160273000-160280800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:160273000-160281000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:160273000-160281000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr3:160273000-160281000	Weak transcription	Fetal Intestine Small	intestine
31	chr3:160273000-160281000	Weak transcription	Right Ventricle	heart
32	chr3:160273000-160281600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:160273400-160281000	Weak transcription	Brain Germinal Matrix	brain
34	chr3:160274200-160282000	Weak transcription	Gastric	stomach
35	chr3:160274600-160279800	Weak transcription	Brain Angular Gyrus	brain
36	chr3:160275800-160279800	Weak transcription	Psoas Muscle	Psoas
37	chr3:160276000-160279600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr3:160276000-160281800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:160276800-160281600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr3:160276800-160281600	Enhancers	Liver	Liver
41	chr3:160276800-160281800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:160276800-160281800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr3:160277000-160279800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:160277000-160281000	Enhancers	Colon Smooth Muscle	Colon
45	chr3:160277200-160281200	Enhancers	Rectal Smooth Muscle	rectum
46	chr3:160277200-160282000	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr3:160277400-160280200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr3:160277400-160280200	Enhancers	Adipose Nuclei	Adipose
49	chr3:160277400-160280800	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr3:160277400-160281000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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