Variant report

Variant	rs10770056
Chromosome Location	chr11:9718324-9718325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10219178	0.83[ASN][1000 genomes]
rs1056593	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs12281578	0.82[ASN][1000 genomes]
rs12421878	0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs12786236	0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs12789209	0.93[EUR][1000 genomes]
rs12801958	0.88[EUR][1000 genomes]
rs12803440	0.82[EUR][1000 genomes]
rs12805683	0.86[EUR][1000 genomes]
rs1496475	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs1532422	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs1836639	0.86[ASN][1000 genomes]
rs2010535	0.82[EUR][1000 genomes]
rs2117698	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2117699	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2164311	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2878800	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs34063054	0.89[EUR][1000 genomes]
rs360047	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360049	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs360051	0.83[ASN][1000 genomes]
rs360054	0.81[ASN][1000 genomes]
rs4548612	0.86[ASN][1000 genomes]
rs4910060	0.86[EUR][1000 genomes]
rs4910489	0.87[ASN][1000 genomes]
rs4910492	0.86[EUR][1000 genomes]
rs4910493	0.89[EUR][1000 genomes]
rs4910497	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs4993191	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61878110	0.82[EUR][1000 genomes]
rs67867011	0.89[EUR][1000 genomes]
rs7113055	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs7114514	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs7116226	0.85[EUR][1000 genomes]
rs7925177	0.82[ASN][1000 genomes]
rs7932792	0.86[ASN][1000 genomes]
rs892851	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs892852	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs892853	0.82[EUR][1000 genomes]
rs892855	0.82[EUR][1000 genomes]
rs892856	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1045550	chr11:9718324-9790088	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10770056	RIC3	cis	cerebellum	SCAN
rs10770056	OR2D2	cis	cerebellum	SCAN
rs10770056	ZNF214	cis	cerebellum	SCAN
rs10770056	MRPL17	cis	cerebellum	SCAN
rs10770056	ASCL3	cis	parietal	SCAN
rs10770056	MRVI1	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9704200-9723600	Weak transcription	HepG2	liver
2	chr11:9710200-9758400	Weak transcription	Psoas Muscle	Psoas
3	chr11:9710400-9732800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:9710600-9722000	Weak transcription	Fetal Brain Female	brain
5	chr11:9711200-9732800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:9711400-9718800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:9711400-9754400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:9711600-9723600	Weak transcription	Fetal Lung	lung
9	chr11:9711600-9724000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr11:9711600-9724400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr11:9711600-9725800	Weak transcription	HSMMtube	muscle
12	chr11:9711600-9729600	Weak transcription	Fetal Heart	heart
13	chr11:9711600-9730200	Weak transcription	Right Ventricle	heart
14	chr11:9711600-9731400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:9711600-9732800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr11:9711600-9733200	Weak transcription	Aorta	Aorta
17	chr11:9711600-9736600	Weak transcription	Gastric	stomach
18	chr11:9711800-9722000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr11:9713400-9724000	Weak transcription	Small Intestine	intestine
20	chr11:9713600-9723800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr11:9713600-9730000	Weak transcription	NH-A	brain
22	chr11:9715000-9718800	Strong transcription	HUVEC	blood vessel
23	chr11:9715000-9718800	Strong transcription	NHDF-Ad	bronchial
24	chr11:9715000-9721600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:9715000-9721800	Weak transcription	Fetal Kidney	kidney
26	chr11:9715200-9720000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr11:9715400-9720000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr11:9715400-9730200	Weak transcription	Pancreas	Pancrea
29	chr11:9715600-9719400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr11:9715600-9719600	Genic enhancers	Primary B cells from cord blood	blood
31	chr11:9715800-9718400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr11:9715800-9718400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:9715800-9719600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr11:9715800-9720200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr11:9715800-9721200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:9715800-9721800	Weak transcription	Brain Substantia Nigra	brain
37	chr11:9715800-9723800	Weak transcription	Fetal Thymus	thymus
38	chr11:9715800-9731200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr11:9715800-9732800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr11:9716000-9721800	Weak transcription	Brain Angular Gyrus	brain
41	chr11:9716000-9721800	Weak transcription	Stomach Mucosa	stomach
42	chr11:9716000-9723600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr11:9716000-9730200	Weak transcription	Esophagus	oesophagus
44	chr11:9716000-9736600	Weak transcription	NHEK	skin
45	chr11:9716000-9738000	Weak transcription	HMEC	breast
46	chr11:9716200-9719600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:9716200-9720200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:9716200-9724000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr11:9716800-9719600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr11:9717200-9719200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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