Variant report

Variant	rs2267676
Chromosome Location	chr6:119531907-119531908
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:119526535..119530412-chr6:119531327..119536580,5	K562	blood:
2	chr6:119531878..119534156-chr6:119544233..119546435,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12209570	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.81[ASN][1000 genomes]
rs12215906	0.90[ASN][1000 genomes]
rs1295391	0.88[ASW][hapmap];0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap]
rs1295392	0.87[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs1324554	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs195048	0.81[ASN][1000 genomes]
rs195056	0.81[EUR][1000 genomes]
rs195090	0.81[ASN][1000 genomes]
rs195092	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[ASN][1000 genomes]
rs2057554	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2267673	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267674	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267675	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299886	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2357164	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778111	0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap]
rs3819731	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4946406	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7755155	0.96[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7755572	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9489630	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9489638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs975578	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv886570	chr6:119450888-119600556	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1034992	chr6:119512657-119540895	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2267676	ASF1A	cis	cerebellum	SCAN
rs2267676	GPRC6A	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119494600-119547400	Weak transcription	Esophagus	oesophagus
2	chr6:119498000-119536600	Weak transcription	Fetal Heart	heart
3	chr6:119503400-119539800	Weak transcription	Gastric	stomach
4	chr6:119516200-119532800	Strong transcription	K562	blood
5	chr6:119519200-119558400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr6:119524200-119532000	Weak transcription	Fetal Brain Male	brain
7	chr6:119524800-119537000	Weak transcription	Pancreas	Pancrea
8	chr6:119524800-119539000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr6:119524800-119558400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:119525000-119535200	Weak transcription	Ovary	ovary
11	chr6:119525200-119534000	Weak transcription	Primary T cells from cord blood	blood
12	chr6:119525400-119533400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:119525400-119537000	Weak transcription	Right Ventricle	heart
14	chr6:119525400-119537400	Weak transcription	Brain Anterior Caudate	brain
15	chr6:119525400-119548600	Weak transcription	Aorta	Aorta
16	chr6:119525400-119556000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:119525400-119558400	Weak transcription	Small Intestine	intestine
18	chr6:119525800-119533400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:119525800-119537000	Weak transcription	Left Ventricle	heart
20	chr6:119525800-119554200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:119525800-119555800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:119526000-119532400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:119526000-119538800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:119526000-119555200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:119526000-119558400	Weak transcription	Placenta	Placenta
26	chr6:119526200-119558400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:119526600-119536400	Weak transcription	Fetal Intestine Large	intestine
28	chr6:119527600-119535200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:119527800-119536400	Weak transcription	Fetal Intestine Small	intestine
30	chr6:119528600-119532600	Enhancers	Fetal Lung	lung
31	chr6:119528600-119551200	Weak transcription	Primary B cells from cord blood	blood
32	chr6:119530000-119532600	Enhancers	Liver	Liver
33	chr6:119530000-119537000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:119530000-119537200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:119530200-119536400	Weak transcription	Fetal Stomach	stomach
36	chr6:119530400-119533800	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:119530600-119532000	Enhancers	GM12878-XiMat	blood
38	chr6:119530800-119532200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:119531000-119532200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:119531000-119536400	Weak transcription	Fetal Kidney	kidney
41	chr6:119531200-119532000	Enhancers	Hela-S3	cervix
42	chr6:119531200-119532200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr6:119531200-119532800	Strong transcription	Primary hematopoietic stem cells	blood
44	chr6:119531200-119552000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:119531400-119532200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:119531400-119532800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:119531400-119532800	Genic enhancers	HepG2	liver
48	chr6:119531400-119537200	Weak transcription	Right Atrium	heart
49	chr6:119531600-119533800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr6:119531600-119535600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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