Variant report

Variant	rs964425
Chromosome Location	chr11:10632484-10632485
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:10618598..10620933-chr11:10630778..10632492,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10219205	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs10219352	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1062912	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10770126	0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10840438	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs10840440	0.90[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs10840441	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs10840443	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10840444	0.85[ASN][1000 genomes]
rs10840445	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10840446	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840448	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840449	0.80[ASN][1000 genomes]
rs11042876	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11042877	0.90[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11042882	0.90[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042883	0.85[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11042893	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11042894	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042895	0.86[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11042897	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042898	0.96[ASN][1000 genomes]
rs11827503	0.96[ASN][1000 genomes]
rs12280275	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12288969	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12576545	0.96[ASN][1000 genomes]
rs12576547	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1531479	0.87[MEX][hapmap];0.82[TSI][hapmap]
rs16907989	0.85[JPT][hapmap]
rs1964537	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2054392	0.92[MEX][hapmap];0.82[TSI][hapmap]
rs2241489	0.94[ASN][1000 genomes]
rs2278124	0.88[CEU][hapmap];0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2278125	0.91[CHD][hapmap]
rs2288236	0.90[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2303402	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34988160	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741033	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3741034	0.81[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs3741042	0.96[ASN][1000 genomes]
rs61892975	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7114453	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7114603	0.94[ASN][1000 genomes]
rs7115310	0.90[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7115735	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7118551	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7126245	0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs724723	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7358373	0.90[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs746164	0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs749045	0.83[ASN][1000 genomes]
rs881436	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs918981	0.81[ASN][1000 genomes]
rs964426	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv832063	chr11:10618485-10785281	ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs964425	RNF141	cis	parietal	SCAN
rs964425	ITGAX	trans	lymphoblastoid	seeQTL
rs964425	MRVI1	cis	brain	seeQTL
rs964425	SNORA45	cis	cerebellum	SCAN
rs964425	MRVI1	cis	normal skin	skin_eQTL
rs964425	MRVI1	cis	multi-tissue	Pritchard
rs964425	MRVI1	trans	brain	seeQTL
rs964425	OVCH2	cis	parietal	SCAN
rs964425	BTBD10	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10595000-10632800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr11:10620200-10635800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:10622800-10632800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr11:10623400-10635400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:10624800-10632800	Enhancers	Thymus	Thymus
6	chr11:10628200-10640200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:10628600-10645600	Weak transcription	Brain Anterior Caudate	brain
8	chr11:10628800-10635800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr11:10629000-10632600	Enhancers	Primary B cells from peripheral blood	blood
10	chr11:10629000-10634800	Enhancers	Primary hematopoietic stem cells	blood
11	chr11:10629000-10640400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:10629200-10632800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:10629200-10635400	Weak transcription	Ovary	ovary
14	chr11:10629200-10635600	Weak transcription	Brain Substantia Nigra	brain
15	chr11:10629400-10635400	Weak transcription	Fetal Intestine Small	intestine
16	chr11:10629400-10635800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:10629400-10635800	Strong transcription	Stomach Smooth Muscle	stomach
18	chr11:10629400-10643800	Weak transcription	Lung	lung
19	chr11:10629400-10644600	Weak transcription	Esophagus	oesophagus
20	chr11:10629400-10650800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr11:10629400-10663600	Weak transcription	Fetal Intestine Large	intestine
22	chr11:10629600-10634800	Weak transcription	Fetal Lung	lung
23	chr11:10629600-10635600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr11:10629600-10662800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr11:10629800-10635800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:10630200-10633800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:10630200-10639200	Weak transcription	Spleen	Spleen
28	chr11:10630800-10645200	Weak transcription	Brain Hippocampus Middle	brain
29	chr11:10631200-10632800	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr11:10631200-10633600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:10631200-10633800	Weak transcription	Stomach Mucosa	stomach
32	chr11:10631400-10635000	Weak transcription	NHLF	lung
33	chr11:10631400-10635200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:10631400-10635400	Weak transcription	Fetal Stomach	stomach
35	chr11:10631800-10632600	Enhancers	Colon Smooth Muscle	Colon
36	chr11:10632000-10633400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr11:10632200-10633400	Genic enhancers	Primary B cells from cord blood	blood
38	chr11:10632200-10635600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr11:10632400-10633400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:10632400-10633400	Weak transcription	Aorta	Aorta

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