Variant report

Variant	rs11583489
Chromosome Location	chr1:227162524-227162525
allele	G/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	chr1:227162361-227162993	HepG2	liver:	n/a	n/a
2	MYBL2	chr1:227162299-227163068	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:227162432-227162945	HepG2	liver:	n/a	n/a
4	RFX5	chr1:227162448-227162959	HepG2	liver:	n/a	n/a
5	MXI1	chr1:227161942-227163062	HepG2	liver:	n/a	chr1:227162106-227162115 chr1:227162104-227162113 chr1:227162104-227162113
6	RCOR1	chr1:227162336-227162999	HepG2	liver:	n/a	n/a
7	RXRA	chr1:227162192-227162540	HepG2	liver:	n/a	chr1:227162373-227162382
8	POLR2A	chr1:227162246-227163144	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ADCK3	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10127638	0.82[CEU][hapmap]
rs1045285	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1045287	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10495256	0.82[CEU][hapmap]
rs11583229	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11588329	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12403775	0.91[CHB][hapmap]
rs12405857	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12593	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1319103	0.92[CHB][hapmap]
rs1343745	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17600747	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17600947	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1929855	0.81[CEU][hapmap];0.93[CHB][hapmap]
rs2297413	0.86[EUR][1000 genomes]
rs2297418	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2297419	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2802271	0.81[CEU][hapmap]
rs3768419	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3768420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3795445	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3795446	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3795449	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4146588	0.82[CEU][hapmap];0.93[CHB][hapmap]
rs6426560	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6677602	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7541033	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7553837	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs938257	0.82[CEU][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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv873236	chr1:227118912-227173537	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv873237	chr1:227118912-227178948	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv873238	chr1:227118912-227180858	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv520923	chr1:227127618-227178948	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227129000-227162600	Weak transcription	Fetal Kidney	kidney
2	chr1:227131000-227171800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:227146400-227162600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:227147000-227177000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:227148600-227180800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:227154200-227164200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:227154400-227165800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
9	chr1:227154600-227163200	Weak transcription	Fetal Thymus	thymus
10	chr1:227154800-227176800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:227158400-227162600	Weak transcription	Thymus	Thymus
12	chr1:227158400-227164600	Weak transcription	Dnd41	blood
13	chr1:227158400-227173200	Weak transcription	K562	blood
14	chr1:227158400-227174600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:227158400-227183000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:227159000-227175800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:227159800-227163800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:227159800-227165800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:227159800-227174000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:227160000-227162600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:227160000-227163000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr1:227160000-227173600	Weak transcription	A549	lung
23	chr1:227160000-227174400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:227160000-227174400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:227160000-227174800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:227160000-227177200	Weak transcription	GM12878-XiMat	blood
27	chr1:227160200-227162800	Enhancers	Placenta	Placenta
28	chr1:227160200-227165200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:227160200-227165200	Enhancers	Liver	Liver
30	chr1:227160400-227163200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr1:227160400-227164600	Enhancers	Right Atrium	heart
32	chr1:227160400-227164800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:227160400-227165200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:227160600-227162600	Enhancers	Aorta	Aorta
35	chr1:227160600-227162600	Enhancers	Esophagus	oesophagus
36	chr1:227160600-227163000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:227160600-227163000	Enhancers	Brain Cingulate Gyrus	brain
38	chr1:227160600-227163200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr1:227160600-227163200	Enhancers	Small Intestine	intestine
40	chr1:227160600-227163400	Enhancers	Fetal Heart	heart
41	chr1:227160600-227163400	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr1:227160600-227163800	Enhancers	Brain Angular Gyrus	brain
43	chr1:227160600-227163800	Enhancers	Fetal Muscle Trunk	muscle
44	chr1:227160600-227163800	Enhancers	Fetal Muscle Leg	muscle
45	chr1:227160600-227163800	Enhancers	Ovary	ovary
46	chr1:227160600-227163800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr1:227160600-227165000	Enhancers	Right Ventricle	heart
48	chr1:227160600-227165400	Enhancers	Left Ventricle	heart
49	chr1:227160600-227165800	Enhancers	Psoas Muscle	Psoas
50	chr1:227160600-227175600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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