Variant report

Variant	rs10839976
Chromosome Location	chr11:8159892-8159893
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10431030	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1055233	0.81[CHD][hapmap]
rs10769869	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10769872	0.80[CEU][hapmap]
rs10769873	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769876	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10769878	0.94[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10839982	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10839984	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10839985	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10839988	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11041742	0.92[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11041757	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11041773	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11607166	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242501	0.84[CEU][hapmap]
rs2242502	0.84[CEU][hapmap]
rs3750955	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4331082	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4340037	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4343012	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4384376	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4397840	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4497397	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7110509	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7941531	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	esv1829170	chr11:8068594-8216369	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv428249	chr11:8068594-8216369	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1048537	chr11:8137353-8196203	Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv896981	chr11:8152080-8227964	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1054339	chr11:8153582-8263173	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10839976	OR52E6	cis	parietal	SCAN
rs10839976	OR52B6	cis	parietal	SCAN
rs10839976	NLRP10	cis	lymphoblastoid	seeQTL
rs10839976	OR10A6	cis	parietal	SCAN
rs10839976	RSPH9	trans	parietal	SCAN
rs10839976	TRIM22	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8126400-8160600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr11:8128800-8162600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:8132600-8160800	Weak transcription	Esophagus	oesophagus
4	chr11:8132600-8172200	Weak transcription	Pancreas	Pancrea
5	chr11:8133600-8162800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr11:8148400-8169200	Weak transcription	Brain Anterior Caudate	brain
7	chr11:8148800-8170200	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:8149400-8162200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr11:8149800-8179600	Weak transcription	Brain Substantia Nigra	brain
10	chr11:8150800-8162600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr11:8152200-8162400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr11:8155200-8166800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:8155400-8160200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:8155800-8163600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr11:8156000-8189800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr11:8156200-8160800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:8156400-8163200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:8156600-8163600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:8157200-8160800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
20	chr11:8157200-8160800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr11:8157200-8161400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:8157200-8162000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr11:8157400-8160800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr11:8157800-8160800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:8157800-8162400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr11:8157800-8162400	Weak transcription	Ovary	ovary
27	chr11:8158000-8161400	Weak transcription	Brain Germinal Matrix	brain
28	chr11:8158000-8161800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr11:8158000-8169600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:8158200-8160200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr11:8158200-8162200	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:8158200-8162400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr11:8158200-8162400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:8158200-8162400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr11:8158200-8162400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr11:8158200-8163200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr11:8158200-8163600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr11:8158400-8160000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr11:8158400-8160600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr11:8158400-8163400	Weak transcription	Brain Angular Gyrus	brain
41	chr11:8158400-8166800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr11:8159200-8160200	Flanking Active TSS	HMEC	breast
43	chr11:8159200-8160600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr11:8159400-8160200	Flanking Active TSS	NHEK	skin
45	chr11:8159400-8160600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr11:8159400-8161000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:8159600-8160200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:8159600-8166800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr11:8159800-8160000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:8159800-8160200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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