Variant report

Variant	rs66577954
Chromosome Location	chr6:25041146-25041147
allele	C/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	RUNX3	chr6:25041036-25041760	GM12878	blood:	n/a	n/a
2	TBP	chr6:25041146-25042953	GM12878	blood:	n/a	n/a
3	NFIC	chr6:25041052-25044467	GM12878	blood:	n/a	n/a
4	ATF2	chr6:25041093-25041774	GM12878	blood:	n/a	n/a
5	PBX3	chr6:25041109-25041814	SK-N-SH	brain:	n/a	n/a
6	MTA3	chr6:25040986-25042896	GM12878	blood:	n/a	n/a
7	CHD1	chr6:25041115-25043023	GM12878	blood:	n/a	n/a
8	WRNIP1	chr6:25041115-25041423	GM12878	blood:	n/a	n/a
9	EBF1	chr6:25041040-25041330	GM12878	blood:	n/a	n/a
10	CEBPB	chr6:25041100-25041901	GM12878	blood:	n/a	n/a
11	MTA3	chr6:25040993-25042553	GM12878	blood:	n/a	n/a
12	PML	chr6:25041080-25042098	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25029897..25032330-chr6:25040931..25043429,2	K562	blood:

Variant related genes	Relation type
ENSG00000229313	TF binding region
ENSG00000244618	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12524842	0.80[ASN][1000 genomes]
rs12525405	0.80[ASN][1000 genomes]
rs12528227	0.80[ASN][1000 genomes]
rs12661796	0.80[ASN][1000 genomes]
rs12663160	0.80[ASN][1000 genomes]
rs12665174	0.80[ASN][1000 genomes]
rs13196712	0.80[ASN][1000 genomes]
rs13218879	0.80[ASN][1000 genomes]
rs1447243	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562422	0.80[ASN][1000 genomes]
rs1562423	0.80[ASN][1000 genomes]
rs1597011	0.80[ASN][1000 genomes]
rs1597012	0.80[ASN][1000 genomes]
rs1900551	0.80[ASN][1000 genomes]
rs1923192	0.80[ASN][1000 genomes]
rs1923193	0.80[ASN][1000 genomes]
rs34475409	0.80[ASN][1000 genomes]
rs35028017	0.80[ASN][1000 genomes]
rs36030790	0.81[ASN][1000 genomes]
rs4712882	0.81[ASN][1000 genomes]
rs67240854	0.80[ASN][1000 genomes]
rs67795839	0.80[ASN][1000 genomes]
rs9348660	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358827	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9393609	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9461093	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25035200-25041200	Weak transcription	Fetal Kidney	kidney
2	chr6:25035200-25044600	Weak transcription	Right Atrium	heart
3	chr6:25036000-25042400	Weak transcription	Lung	lung
4	chr6:25036600-25041200	Weak transcription	NH-A	brain
5	chr6:25036600-25041800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr6:25038600-25041200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:25038600-25041400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr6:25038600-25042200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr6:25039000-25041400	Enhancers	Primary B cells from cord blood	blood
10	chr6:25039000-25041400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:25039000-25042000	Flanking Active TSS	Dnd41	blood
12	chr6:25039000-25043800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:25039400-25041400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr6:25039400-25041800	Weak transcription	Small Intestine	intestine
15	chr6:25039600-25041200	Weak transcription	Spleen	Spleen
16	chr6:25039600-25041200	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr6:25039800-25041400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr6:25040000-25041400	Weak transcription	Fetal Heart	heart
19	chr6:25040200-25043000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr6:25040400-25041400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:25040600-25041400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:25040600-25041400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr6:25040600-25042800	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr6:25040600-25043200	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr6:25040800-25041400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:25040800-25042600	Active TSS	Thymus	Thymus
27	chr6:25041000-25041200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:25041000-25041400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:25041000-25041400	Flanking Active TSS	GM12878-XiMat	blood
30	chr6:25041000-25041600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:25041000-25041600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr6:25041000-25041800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr6:25041000-25041800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr6:25041000-25042000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr6:25041000-25042200	Enhancers	Fetal Lung	lung
36	chr6:25041000-25042200	Enhancers	HUVEC	blood vessel
37	chr6:25041000-25042400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:25041000-25042600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:25041000-25042800	Active TSS	Duodenum Mucosa	Duodenum
40	chr6:25041000-25042800	Flanking Active TSS	Fetal Thymus	thymus
41	chr6:25041000-25042800	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr6:25041000-25043000	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr6:25041000-25043000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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