Variant report

Variant	rs2817725
Chromosome Location	chr6:24901350-24901351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24895200..24897820-chr6:24899260..24901448,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2064524	0.84[JPT][hapmap]
rs2747677	0.85[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2747682	0.89[YRI][hapmap]
rs2747683	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2817718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2817720	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2817722	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[ASN][1000 genomes]
rs2817723	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2817724	0.83[ASN][1000 genomes]
rs2817726	0.86[ASN][1000 genomes]
rs734014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs734015	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs932494	0.84[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24876000-24901800	Weak transcription	Spleen	Spleen
2	chr6:24882400-24904000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:24884000-24908200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:24891000-24902800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:24891600-24901400	Weak transcription	GM12878-XiMat	blood
6	chr6:24891600-24901800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:24891600-24908400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:24896400-24902600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
9	chr6:24896400-24908600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr6:24897400-24901400	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr6:24897400-24903800	Genic enhancers	Primary B cells from cord blood	blood
12	chr6:24897400-24904800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:24897400-24907600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:24897400-24909600	Genic enhancers	Primary B cells from peripheral blood	blood
15	chr6:24897800-24901400	Weak transcription	HSMM	muscle
16	chr6:24898400-24903800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:24898600-24901800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:24898800-24904200	Enhancers	NHDF-Ad	bronchial
19	chr6:24899000-24904400	Weak transcription	Stomach Mucosa	stomach
20	chr6:24899000-24908200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:24899200-24902400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
22	chr6:24899200-24902800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:24899400-24902000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr6:24899800-24901800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:24899800-24902000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:24899800-24909600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:24900000-24903400	Genic enhancers	Fetal Thymus	thymus
28	chr6:24900000-24903600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:24900000-24906000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr6:24900000-24909000	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr6:24900200-24901800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr6:24900200-24901800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:24900200-24902000	Enhancers	Fetal Muscle Leg	muscle
34	chr6:24900200-24903000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:24900200-24909800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:24900400-24901400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:24900400-24901400	Weak transcription	Colonic Mucosa	Colon
38	chr6:24900400-24901400	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr6:24900400-24901800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:24900400-24901800	Weak transcription	Brain Substantia Nigra	brain
41	chr6:24900400-24902200	Weak transcription	Thymus	Thymus
42	chr6:24900400-24904000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr6:24900400-24907800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr6:24900400-24908200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr6:24900400-24908200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr6:24900400-24908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:24900600-24904000	Weak transcription	Aorta	Aorta
48	chr6:24900600-24904600	Genic enhancers	Primary T cells from cord blood	blood
49	chr6:24900600-24905600	Weak transcription	Brain Anterior Caudate	brain
50	chr6:24900600-24907200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood

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