Variant report

Variant	rs9356959
Chromosome Location	chr6:25041991-25041992
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	STAT5A	chr6:25041812-25042833	GM12878	blood:	n/a	chr6:25042774-25042785
2	NFIC	chr6:25041953-25042616	GM12878	blood:	n/a	n/a
3	TBP	chr6:25041146-25042953	GM12878	blood:	n/a	n/a
4	NFIC	chr6:25041052-25044467	GM12878	blood:	n/a	n/a
5	IKZF1	chr6:25041229-25042304	GM12878	blood:	n/a	n/a
6	TBL1XR1	chr6:25041258-25042820	GM12878	blood:	n/a	n/a
7	WRNIP1	chr6:25041896-25042676	GM12878	blood:	n/a	n/a
8	BATF	chr6:25041908-25042201	GM12878	blood:	n/a	n/a
9	MTA3	chr6:25040986-25042896	GM12878	blood:	n/a	n/a
10	CHD1	chr6:25041115-25043023	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:25041928-25043097	Raji	blood:	n/a	n/a
12	ZNF384	chr6:25041943-25042526	GM12878	blood:	n/a	n/a
13	FOXM1	chr6:25041310-25042110	GM12878	blood:	n/a	n/a
14	MTA3	chr6:25040993-25042553	GM12878	blood:	n/a	n/a
15	GATA1	chr6:25041232-25042000	PBDE	blood:	n/a	chr6:25041680-25041689
16	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: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs3749875	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73729424	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73732206	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358828	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366600	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379709	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461095	0.83[AMR][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:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25035200-25044600	Weak transcription	Right Atrium	heart
2	chr6:25036000-25042400	Weak transcription	Lung	lung
3	chr6:25038600-25042200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr6:25039000-25042000	Flanking Active TSS	Dnd41	blood
5	chr6:25039000-25043800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:25040200-25043000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr6:25040600-25042800	Flanking Active TSS	Primary B cells from peripheral blood	blood
8	chr6:25040600-25043200	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr6:25040800-25042600	Active TSS	Thymus	Thymus
10	chr6:25041000-25042000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
11	chr6:25041000-25042200	Enhancers	Fetal Lung	lung
12	chr6:25041000-25042200	Enhancers	HUVEC	blood vessel
13	chr6:25041000-25042400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:25041000-25042600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:25041000-25042800	Active TSS	Duodenum Mucosa	Duodenum
16	chr6:25041000-25042800	Flanking Active TSS	Fetal Thymus	thymus
17	chr6:25041000-25042800	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr6:25041000-25043000	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr6:25041000-25043000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr6:25041200-25042600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:25041200-25042600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr6:25041200-25042600	Active TSS	Rectal Smooth Muscle	rectum
23	chr6:25041200-25042800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:25041200-25043000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr6:25041400-25042200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:25041400-25042200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:25041400-25042400	Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr6:25041400-25042400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:25041400-25042400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:25041400-25042800	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr6:25041400-25043200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr6:25041600-25042000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:25041600-25042000	Active TSS	Fetal Kidney	kidney
34	chr6:25041600-25042600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:25041800-25042000	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr6:25041800-25042000	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr6:25041800-25042000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr6:25041800-25042000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:25041800-25042000	Enhancers	Fetal Heart	heart
40	chr6:25041800-25042000	Enhancers	Small Intestine	intestine
41	chr6:25041800-25042000	Active TSS	GM12878-XiMat	blood
42	chr6:25041800-25042200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr6:25041800-25042600	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr6:25041800-25042800	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr6:25041800-25042800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr6:25041800-25042800	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr6:25041800-25043200	Enhancers	Spleen	Spleen
48	chr6:25041800-25043400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:25041800-25044000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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