Variant report

Variant	rs9474687
Chromosome Location	chr6:53795480-53795481
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	chr6:53794903..53796412-chr6:53797970..53799605,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10456674	0.91[YRI][hapmap]
rs10948787	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11751301	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12204130	0.91[YRI][hapmap]
rs12663216	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs13437448	0.92[EUR][1000 genomes]
rs1883632	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs2076496	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2076497	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3003492	0.87[CEU][hapmap];0.84[CHB][hapmap]
rs3003498	0.91[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.84[TSI][hapmap]
rs3813850	0.91[GIH][hapmap]
rs4486000	0.91[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.83[TSI][hapmap]
rs4712050	0.92[EUR][1000 genomes]
rs4712051	0.91[EUR][1000 genomes]
rs5006063	0.93[EUR][1000 genomes]
rs61068246	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62396285	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6905563	0.94[CEU][hapmap]
rs6927232	0.92[EUR][1000 genomes]
rs763813	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs763815	0.92[EUR][1000 genomes]
rs7750173	0.83[EUR][1000 genomes]
rs9296727	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9474687	C6orf142	cis	cerebellum	SCAN
rs9474687	BAG2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53768800-53796000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:53770000-53795800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:53772000-53803000	Weak transcription	Lung	lung
4	chr6:53787800-53796000	Weak transcription	Primary T cells from cord blood	blood
5	chr6:53787800-53807800	Weak transcription	Aorta	Aorta
6	chr6:53787800-53810800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:53790600-53797200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:53790600-53798000	Weak transcription	Fetal Thymus	thymus
9	chr6:53791000-53795600	Weak transcription	Brain Germinal Matrix	brain
10	chr6:53791000-53795800	Weak transcription	Brain Substantia Nigra	brain
11	chr6:53791000-53796200	Enhancers	HUVEC	blood vessel
12	chr6:53792200-53795600	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:53792200-53795800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:53792800-53796600	Weak transcription	Placenta	Placenta
15	chr6:53792800-53797800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:53793000-53799200	Weak transcription	HSMMtube	muscle
17	chr6:53793600-53797000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:53794200-53795600	Weak transcription	HepG2	liver
19	chr6:53794400-53795600	Enhancers	Right Ventricle	heart
20	chr6:53794400-53795800	Enhancers	Esophagus	oesophagus
21	chr6:53794600-53801000	Weak transcription	Dnd41	blood
22	chr6:53794600-53807800	Weak transcription	Left Ventricle	heart
23	chr6:53794800-53803200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:53794800-53815600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:53795000-53795600	Genic enhancers	NHEK	skin
26	chr6:53795000-53797200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:53795000-53797200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr6:53795200-53797000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:53795200-53797200	Weak transcription	Fetal Intestine Small	intestine
30	chr6:53795200-53797600	Weak transcription	Small Intestine	intestine
31	chr6:53795200-53799200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:53795200-53803800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:53795200-53807400	Weak transcription	Fetal Stomach	stomach
34	chr6:53795400-53799200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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