Variant report

Variant	rs2814894
Chromosome Location	chr6:38544497-38544498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38542008..38544985-chr6:38545718..38547507,2	K562	blood:
2	chr6:38538560..38540420-chr6:38542934..38544675,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10807196	0.84[ASW][hapmap];0.96[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs10807198	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10947752	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1321056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699001	1.00[CEU][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1699002	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1699003	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1699004	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1699005	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1699007	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1699017	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1739621	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1739626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1739627	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs1739628	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1739629	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1739630	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1739632	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1739633	0.82[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1781708	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1781711	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1781712	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1852979	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2092797	0.81[CHD][hapmap]
rs2144328	0.89[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2180104	0.81[EUR][1000 genomes]
rs2252550	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2748165	0.83[EUR][1000 genomes]
rs2748172	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2814883	1.00[ASW][hapmap];0.92[CEU][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2814885	0.84[EUR][1000 genomes]
rs2814889	0.84[ASW][hapmap];0.92[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4236060	0.82[ASW][hapmap]
rs4392718	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs6458059	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6931131	0.81[CHD][hapmap]
rs910516	1.00[CEU][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394521	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2814894	GLO1	cis	cerebellum	SCAN
rs2814894	BYSL	cis	cerebellum	SCAN
rs2814894	DNAH8	cis	cerebellum	SCAN
rs2814894	GLO1	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38510600-38546800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:38519600-38554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:38523000-38571600	Weak transcription	HSMMtube	muscle
4	chr6:38532400-38547800	Weak transcription	Fetal Kidney	kidney
5	chr6:38533200-38547000	Weak transcription	Aorta	Aorta
6	chr6:38534200-38544800	Weak transcription	Fetal Intestine Large	intestine
7	chr6:38534400-38561600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr6:38534800-38547000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:38535400-38554600	Weak transcription	Fetal Stomach	stomach
10	chr6:38535600-38544800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:38535600-38547000	Weak transcription	Brain Substantia Nigra	brain
12	chr6:38535600-38547000	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:38535600-38555400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:38535600-38555800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:38535600-38556000	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:38535600-38556000	Weak transcription	NHLF	lung
17	chr6:38535600-38557600	Weak transcription	HSMM	muscle
18	chr6:38535800-38547800	Weak transcription	Osteobl	bone
19	chr6:38535800-38548000	Weak transcription	Fetal Heart	heart
20	chr6:38535800-38559800	Weak transcription	Fetal Lung	lung
21	chr6:38535800-38560200	Weak transcription	NH-A	brain
22	chr6:38535800-38564000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:38535800-38578200	Weak transcription	Colon Smooth Muscle	Colon
24	chr6:38536000-38546800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:38536200-38556000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:38536200-38559200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:38536400-38555800	Weak transcription	NHDF-Ad	bronchial
28	chr6:38536400-38560200	Weak transcription	Brain Angular Gyrus	brain
29	chr6:38536800-38566400	Weak transcription	Pancreas	Pancrea
30	chr6:38537000-38557200	Weak transcription	Thymus	Thymus
31	chr6:38538000-38566800	Weak transcription	Esophagus	oesophagus
32	chr6:38538200-38558600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:38538600-38548000	Weak transcription	Fetal Intestine Small	intestine
34	chr6:38538600-38561800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr6:38538600-38562000	Weak transcription	Brain Germinal Matrix	brain
36	chr6:38539000-38545800	Weak transcription	Brain Anterior Caudate	brain
37	chr6:38539800-38545800	Weak transcription	Left Ventricle	heart
38	chr6:38539800-38554800	Weak transcription	Lung	lung
39	chr6:38539800-38562800	Weak transcription	Fetal Thymus	thymus
40	chr6:38540000-38548000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:38540200-38544800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:38540200-38547800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:38540400-38545000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr6:38540400-38545800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:38540400-38549000	Weak transcription	Dnd41	blood
46	chr6:38540400-38552600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr6:38540400-38557800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:38540400-38560000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr6:38540400-38561600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr6:38540400-38567800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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