Variant report

Variant	rs9358827
Chromosome Location	chr6:25037672-25037673
allele	C/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	WRNIP1	chr6:25037010-25037685	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25032692..25035035-chr6:25036206..25038734,3	K562	blood:
2	chr6:24895729..24898166-chr6:25036279..25038018,2	K562	blood:

Variant related genes	Relation type
ENSG00000229313	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12661796	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs12665174	0.94[JPT][hapmap]
rs1447243	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1562422	0.94[JPT][hapmap]
rs1562423	0.94[JPT][hapmap]
rs1597010	0.94[JPT][hapmap]
rs1597011	0.94[JPT][hapmap]
rs1900551	0.94[JPT][hapmap]
rs4711071	0.94[JPT][hapmap]
rs4711073	0.94[JPT][hapmap]
rs4712882	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs66577954	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9348660	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9393609	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461093	1.00[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]

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	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	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	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
6	esv3368813	chr6:25037670-25038121	Weak transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9358827	SLC17A4	cis	cerebellum	SCAN
rs9358827	HIST1H1E	cis	parietal	SCAN
rs9358827	HIST1H3I	cis	parietal	SCAN
rs9358827	HIST1H2BG	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25034600-25038600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:25035200-25041200	Weak transcription	Fetal Kidney	kidney
3	chr6:25035200-25044600	Weak transcription	Right Atrium	heart
4	chr6:25035800-25037800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:25035800-25039400	Weak transcription	Liver	Liver
6	chr6:25035800-25040600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:25035800-25041000	Enhancers	Fetal Thymus	thymus
8	chr6:25036000-25038800	Weak transcription	Spleen	Spleen
9	chr6:25036000-25042400	Weak transcription	Lung	lung
10	chr6:25036400-25038000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr6:25036400-25038000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:25036400-25038600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr6:25036400-25039000	Enhancers	Primary hematopoietic stem cells	blood
14	chr6:25036400-25040600	Enhancers	Primary B cells from peripheral blood	blood
15	chr6:25036400-25041000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:25036400-25041000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:25036600-25038000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr6:25036600-25038000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr6:25036600-25038800	Weak transcription	Primary T cells from cord blood	blood
20	chr6:25036600-25038800	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr6:25036600-25039000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:25036600-25039400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:25036600-25040600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:25036600-25041200	Weak transcription	NH-A	brain
25	chr6:25036600-25041800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr6:25037000-25038600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:25037000-25038600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr6:25037000-25038800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:25037000-25041000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr6:25037200-25037800	Flanking Active TSS	Dnd41	blood
31	chr6:25037200-25039000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr6:25037400-25038600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr6:25037400-25038800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:25037600-25037800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:25037600-25037800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:25037600-25038000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:25037600-25039000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr6:25037600-25039000	Weak transcription	Thymus	Thymus

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