Variant report

Variant	rs972594
Chromosome Location	chr11:9510715-9510716
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: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1020621	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1020622	0.81[ASN][1000 genomes]
rs10770028	0.95[JPT][hapmap]
rs10770032	0.95[JPT][hapmap]
rs10770033	0.81[ASN][1000 genomes]
rs10770034	0.95[ASN][1000 genomes]
rs10770037	0.87[CHD][hapmap]
rs10840228	0.95[JPT][hapmap]
rs10840234	0.89[JPT][hapmap]
rs10840235	0.90[JPT][hapmap]
rs10840238	0.81[ASN][1000 genomes]
rs10840243	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10840244	0.87[ASN][1000 genomes]
rs10840245	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10840247	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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	0.81[ASN][1000 genomes]
rs11042355	0.81[ASN][1000 genomes]
rs11042356	0.81[ASN][1000 genomes]
rs11042366	0.95[JPT][hapmap]
rs11042374	0.89[ASN][1000 genomes]
rs11042377	0.95[ASN][1000 genomes]
rs11042393	0.95[ASN][1000 genomes]
rs11042395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11601316	0.95[ASN][1000 genomes]
rs12271897	0.81[ASN][1000 genomes]
rs12282176	0.81[ASN][1000 genomes]
rs12792161	0.96[ASN][1000 genomes]
rs12795344	0.95[JPT][hapmap]
rs12800802	0.81[ASN][1000 genomes]
rs12806418	0.96[ASN][1000 genomes]
rs1377667	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1470895	0.96[ASN][1000 genomes]
rs1470896	0.99[ASN][1000 genomes]
rs1543	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1968717	0.95[ASN][1000 genomes]
rs2278900	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2290423	0.90[JPT][hapmap]
rs2290424	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2290425	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3763874	0.87[CHD][hapmap]
rs3763876	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3763877	0.99[ASN][1000 genomes]
rs41369549	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4625466	0.90[JPT][hapmap]
rs4810	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4910053	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4910468	0.99[ASN][1000 genomes]
rs4910472	0.81[ASN][1000 genomes]
rs6486307	0.95[JPT][hapmap]
rs6486359	0.81[ASN][1000 genomes]
rs6486361	0.88[ASW][hapmap];0.86[CEU][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6486394	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]
rs67548305	0.81[ASN][1000 genomes]
rs7102473	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7104568	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7122252	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs723297	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs727405	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs729313	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7395411	0.81[ASN][1000 genomes]
rs7483667	0.95[ASN][1000 genomes]
rs7926589	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7927350	0.90[JPT][hapmap]
rs7933621	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7939724	0.87[CHD][hapmap]
rs7944578	0.90[JPT][hapmap]
rs7949973	0.81[ASN][1000 genomes]
rs8785	0.95[JPT][hapmap];0.81[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs972594	GVIN1	cis	parietal	SCAN
rs972594	CYB5R2	cis	parietal	SCAN
rs972594	SNORA23	cis	parietal	SCAN
rs972594	IPO7	Cis_1M	lymphoblastoid	RTeQTL
rs972594	OR56A1	cis	cerebellum	SCAN

Chromatin state (count:125 , 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	chr11:9501800-9510800	Weak transcription	HMEC	breast
27	chr11:9501800-9511600	Weak transcription	Ovary	ovary
28	chr11:9501800-9515800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr11:9501800-9516000	Weak transcription	Brain Angular Gyrus	brain
30	chr11:9501800-9516000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:9501800-9517200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:9501800-9517200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr11:9501800-9534000	Weak transcription	Psoas Muscle	Psoas
34	chr11:9502200-9516000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:9502800-9517200	Weak transcription	Colonic Mucosa	Colon
36	chr11:9503000-9512200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:9503000-9512200	Weak transcription	Spleen	Spleen
38	chr11:9503000-9512400	Weak transcription	HepG2	liver
39	chr11:9503000-9515600	Weak transcription	Brain Hippocampus Middle	brain
40	chr11:9503000-9516400	Weak transcription	Brain Substantia Nigra	brain
41	chr11:9503000-9517200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr11:9503000-9519600	Weak transcription	Gastric	stomach
43	chr11:9503000-9521000	Weak transcription	Aorta	Aorta
44	chr11:9503400-9512200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr11:9503800-9514000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr11:9504200-9513400	Strong transcription	Fetal Thymus	thymus
47	chr11:9504600-9513400	Strong transcription	Stomach Smooth Muscle	stomach
48	chr11:9505200-9525200	Strong transcription	Placenta	Placenta
49	chr11:9505600-9513000	Weak transcription	Right Ventricle	heart
50	chr11:9506000-9525200	Strong transcription	Primary T cells fromperipheralblood	blood

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