Variant report

Variant	rs6486394
Chromosome Location	chr11:9512121-9512122
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	chr11:9510455..9512586-chr11:9513778..9516603,2	K562	blood:
2	chr11:9510653..9512629-chr11:9515570..9517732,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1020621	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1020622	0.82[ASN][1000 genomes]
rs10770028	0.95[JPT][hapmap]
rs10770032	0.95[JPT][hapmap]
rs10770033	0.82[ASN][1000 genomes]
rs10770034	0.95[ASN][1000 genomes]
rs10770037	0.90[CHD][hapmap]
rs10840228	0.95[JPT][hapmap]
rs10840234	0.89[JPT][hapmap]
rs10840235	0.90[JPT][hapmap]
rs10840237	0.80[ASN][1000 genomes]
rs10840238	0.81[ASN][1000 genomes]
rs10840243	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10840244	0.88[ASN][1000 genomes]
rs10840245	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10840247	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840249	0.98[ASN][1000 genomes]
rs10840253	0.81[JPT][hapmap]
rs11042328	0.95[JPT][hapmap]
rs11042329	0.85[JPT][hapmap]
rs11042350	0.81[ASN][1000 genomes]
rs11042353	0.82[ASN][1000 genomes]
rs11042355	0.82[ASN][1000 genomes]
rs11042356	0.82[ASN][1000 genomes]
rs11042366	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs11042374	0.90[ASN][1000 genomes]
rs11042377	0.95[ASN][1000 genomes]
rs11042393	0.96[ASN][1000 genomes]
rs11042395	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11601316	0.95[ASN][1000 genomes]
rs12271897	0.81[ASN][1000 genomes]
rs12282176	0.82[ASN][1000 genomes]
rs12792161	0.97[ASN][1000 genomes]
rs12795344	0.95[JPT][hapmap]
rs12800802	0.81[ASN][1000 genomes]
rs12806418	0.97[ASN][1000 genomes]
rs1377667	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470895	0.97[ASN][1000 genomes]
rs1470896	1.00[ASN][1000 genomes]
rs1543	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1968717	0.95[ASN][1000 genomes]
rs2278900	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2290423	0.90[JPT][hapmap]
rs2290424	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2290425	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs35781320	0.80[ASN][1000 genomes]
rs3763874	0.90[CHD][hapmap]
rs3763876	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3763877	1.00[ASN][1000 genomes]
rs41369549	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4625466	0.90[JPT][hapmap]
rs4810	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4910053	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4910468	1.00[ASN][1000 genomes]
rs4910472	0.81[ASN][1000 genomes]
rs6486307	0.95[JPT][hapmap]
rs6486359	0.82[ASN][1000 genomes]
rs6486361	0.88[ASW][hapmap];0.90[CEU][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67548305	0.82[ASN][1000 genomes]
rs7102473	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7104568	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7122252	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs723297	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727405	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs729313	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7395411	0.81[ASN][1000 genomes]
rs7483667	0.95[ASN][1000 genomes]
rs7926589	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7927350	0.90[JPT][hapmap]
rs7933621	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7939724	0.90[CHD][hapmap]
rs7944578	0.90[JPT][hapmap]
rs7949973	0.82[ASN][1000 genomes]
rs8785	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs972594	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][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	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh 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	89 gene(s)	inside rSNPs	diseases
3	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv1039537	chr11:9455387-9535970	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv7670	chr11:9500895-9514750	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6486394	OR56A1	cis	cerebellum	SCAN
rs6486394	OR56A4	cis	cerebellum	SCAN
rs6486394	SNORA23	cis	parietal	SCAN
rs6486394	GVIN1	cis	parietal	SCAN
rs6486394	CYB5R2	cis	parietal	SCAN
rs6486394	IPO7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9483600-9518600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:9484600-9544800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:9485200-9520000	Weak transcription	Stomach Mucosa	stomach
4	chr11:9489600-9524000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr11:9489800-9523400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr11:9491400-9525400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr11:9491400-9551600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:9492000-9527200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:9492200-9525400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:9492800-9527800	Strong transcription	Fetal Stomach	stomach
11	chr11:9495600-9525400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:9496200-9520000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:9496200-9522600	Weak transcription	Fetal Heart	heart
14	chr11:9496600-9516000	Weak transcription	Fetal Brain Male	brain
15	chr11:9496600-9517000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:9496600-9528200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:9497400-9517400	Weak transcription	Small Intestine	intestine
18	chr11:9499200-9526000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:9500200-9516000	Weak transcription	Pancreas	Pancrea
20	chr11:9500400-9522600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:9500600-9519800	Weak transcription	A549	lung
22	chr11:9501400-9512400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:9501400-9522600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:9501600-9517400	Weak transcription	Esophagus	oesophagus
25	chr11:9501600-9519800	Weak transcription	Fetal Kidney	kidney
26	chr11:9501800-9515800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr11:9501800-9516000	Weak transcription	Brain Angular Gyrus	brain
28	chr11:9501800-9516000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr11:9501800-9517200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:9501800-9517200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr11:9501800-9534000	Weak transcription	Psoas Muscle	Psoas
32	chr11:9502200-9516000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr11:9502800-9517200	Weak transcription	Colonic Mucosa	Colon
34	chr11:9503000-9512200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:9503000-9512200	Weak transcription	Spleen	Spleen
36	chr11:9503000-9512400	Weak transcription	HepG2	liver
37	chr11:9503000-9515600	Weak transcription	Brain Hippocampus Middle	brain
38	chr11:9503000-9516400	Weak transcription	Brain Substantia Nigra	brain
39	chr11:9503000-9517200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr11:9503000-9519600	Weak transcription	Gastric	stomach
41	chr11:9503000-9521000	Weak transcription	Aorta	Aorta
42	chr11:9503400-9512200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr11:9503800-9514000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr11:9504200-9513400	Strong transcription	Fetal Thymus	thymus
45	chr11:9504600-9513400	Strong transcription	Stomach Smooth Muscle	stomach
46	chr11:9505200-9525200	Strong transcription	Placenta	Placenta
47	chr11:9505600-9513000	Weak transcription	Right Ventricle	heart
48	chr11:9506000-9525200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr11:9506800-9514000	Strong transcription	Primary T cells from cord blood	blood
50	chr11:9506800-9517400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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