Variant report

Variant	rs7117813
Chromosome Location	chr11:77552534-77552535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1045590	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11820337	0.86[ASW][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs12225188	0.95[YRI][hapmap]
rs12417115	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1793340	0.81[ASN][1000 genomes]
rs2186562	0.89[YRI][hapmap]
rs28653530	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4145700	0.89[CHD][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs516529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55190	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs567814	0.86[ASW][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs569072	0.93[ASW][hapmap];0.95[CEU][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes]
rs572541	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs585513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs616354	0.86[ASW][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs634477	0.81[ASN][1000 genomes]
rs648842	0.84[YRI][hapmap]
rs650636	0.86[ASW][hapmap];0.89[CHD][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs665363	0.89[YRI][hapmap]
rs681411	0.89[YRI][hapmap]
rs7115444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7118800	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7119332	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7129325	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7931137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7932547	0.83[JPT][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7117813	NEU3	cis	parietal	SCAN
rs7117813	RSF1	cis	parietal	SCAN
rs7117813	DNAJB13	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77533000-77553800	Weak transcription	Brain Angular Gyrus	brain
2	chr11:77533000-77554000	Weak transcription	Brain Substantia Nigra	brain
3	chr11:77533000-77554200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:77533400-77553800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:77533400-77554000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr11:77533400-77565600	Weak transcription	Gastric	stomach
7	chr11:77533400-77565600	Weak transcription	Pancreas	Pancrea
8	chr11:77533600-77553000	Weak transcription	HUVEC	blood vessel
9	chr11:77534600-77555400	Weak transcription	Lung	lung
10	chr11:77535200-77552800	Weak transcription	Aorta	Aorta
11	chr11:77535200-77553800	Weak transcription	NHDF-Ad	bronchial
12	chr11:77535200-77554200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr11:77535200-77554400	Weak transcription	HSMM	muscle
14	chr11:77535400-77553400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:77535400-77553400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr11:77535400-77554200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr11:77535400-77555000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:77535400-77565600	Weak transcription	HepG2	liver
19	chr11:77541600-77553800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:77544600-77552600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:77544600-77555400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr11:77544600-77564400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr11:77544600-77565400	Weak transcription	Spleen	Spleen
24	chr11:77544800-77553400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:77544800-77554200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr11:77544800-77554200	Weak transcription	Dnd41	blood
27	chr11:77544800-77554400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:77544800-77564400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:77544800-77565400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr11:77545000-77554000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:77545000-77555400	Weak transcription	Fetal Kidney	kidney
32	chr11:77547200-77565800	Weak transcription	Fetal Heart	heart
33	chr11:77547600-77555200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr11:77548800-77582800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:77549000-77553400	Weak transcription	NH-A	brain
36	chr11:77549200-77552800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr11:77549400-77552600	Weak transcription	Right Ventricle	heart
38	chr11:77550000-77565600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:77550200-77553000	Weak transcription	Osteobl	bone
40	chr11:77550200-77553400	Weak transcription	Primary T cells from cord blood	blood
41	chr11:77550200-77554000	Weak transcription	Brain Anterior Caudate	brain
42	chr11:77550400-77554200	Weak transcription	HSMMtube	muscle
43	chr11:77550400-77557200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:77550800-77554200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr11:77550800-77564000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr11:77550800-77565400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr11:77551000-77555400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr11:77551200-77558400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr11:77551400-77565400	Weak transcription	Fetal Thymus	thymus
50	chr11:77551600-77553000	ZNF genes & repeats	Fetal Intestine Small	intestine

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