Variant report

Variant	rs7929313
Chromosome Location	chr11:77606217-77606218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs108843	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10899414	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11237264	0.80[ASN][1000 genomes]
rs11237279	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12294668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1783547	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2508184	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35711367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4945228	0.94[ASW][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap]
rs570786	0.91[EUR][1000 genomes]
rs581807	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs582866	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs584732	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs585172	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs585721	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs591283	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs598933	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs600968	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs601551	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs603462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs608389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs608539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs609151	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs611671	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs611906	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs636041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs647235	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs649671	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs658398	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs667213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs679155	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs679526	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs685474	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs694893	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7936105	0.93[ASN][1000 genomes]
rs9667706	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1035753	chr11:77577384-77866386	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv541093	chr11:77577384-77866386	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv555453	chr11:77577494-77618441	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv975954	chr11:77600915-77617903	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7929313	ALG8	cis	parietal	SCAN
rs7929313	THRSP	cis	cerebellum	SCAN
rs7929313	AQP11	cis	parietal	SCAN
rs7929313	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs7929313	NDUFC2	cis	cerebellum	SCAN
rs7929313	ALG8	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77577400-77630800	Weak transcription	Fetal Heart	heart
2	chr11:77579200-77625000	Weak transcription	HMEC	breast
3	chr11:77583400-77670600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:77583400-77690000	Weak transcription	Colonic Mucosa	Colon
5	chr11:77586600-77625000	Weak transcription	Stomach Mucosa	stomach
6	chr11:77587200-77617600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:77588200-77614000	Weak transcription	Right Ventricle	heart
8	chr11:77591800-77650400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
10	chr11:77593800-77625000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr11:77595400-77620000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr11:77595800-77671000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr11:77597400-77617400	Weak transcription	Brain Hippocampus Middle	brain
14	chr11:77597400-77625000	Weak transcription	A549	lung
15	chr11:77597600-77617400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:77597600-77629400	Weak transcription	Brain Germinal Matrix	brain
17	chr11:77597800-77609600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:77597800-77612200	Weak transcription	Brain Anterior Caudate	brain
19	chr11:77597800-77613600	Weak transcription	Fetal Intestine Large	intestine
20	chr11:77597800-77614000	Weak transcription	Lung	lung
21	chr11:77597800-77614000	Weak transcription	HSMMtube	muscle
22	chr11:77597800-77614200	Weak transcription	Brain Angular Gyrus	brain
23	chr11:77597800-77614200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr11:77597800-77614400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:77597800-77617400	Weak transcription	GM12878-XiMat	blood
26	chr11:77597800-77617600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr11:77597800-77617600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:77597800-77617800	Weak transcription	Fetal Kidney	kidney
29	chr11:77597800-77620000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr11:77597800-77624800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:77597800-77625000	Weak transcription	Colon Smooth Muscle	Colon
32	chr11:77597800-77625000	Weak transcription	Pancreas	Pancrea
33	chr11:77597800-77625000	Weak transcription	NHDF-Ad	bronchial
34	chr11:77597800-77625200	Weak transcription	NHEK	skin
35	chr11:77597800-77625600	Weak transcription	HSMM	muscle
36	chr11:77597800-77629000	Weak transcription	Aorta	Aorta
37	chr11:77597800-77633800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr11:77597800-77644200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:77597800-77644400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:77597800-77669800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr11:77597800-77671000	Weak transcription	Fetal Brain Male	brain
42	chr11:77597800-77678200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr11:77597800-77690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:77597800-77690000	Weak transcription	Esophagus	oesophagus
45	chr11:77597800-77690000	Weak transcription	Gastric	stomach
46	chr11:77600600-77606400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr11:77600600-77606400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr11:77600800-77608000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr11:77601000-77618000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:77601400-77611400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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