Variant report

Variant	rs7946709
Chromosome Location	chr11:47100796-47100797
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10466478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10501319	0.83[CHB][hapmap];0.92[GIH][hapmap]
rs1055447	0.81[GIH][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs1060573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769225	0.82[CHB][hapmap]
rs10769226	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs10769227	0.83[CHB][hapmap]
rs10769230	0.89[ASN][1000 genomes]
rs10769233	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769239	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10838635	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs10838640	0.83[CHB][hapmap]
rs10838644	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs10838646	0.83[CHB][hapmap]
rs10838652	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs10838654	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838658	0.82[CHB][hapmap]
rs10838659	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10838660	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10838662	0.83[CHB][hapmap];0.92[GIH][hapmap]
rs10838663	0.83[CHB][hapmap]
rs10838664	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs11039035	0.83[CHB][hapmap]
rs11039074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039086	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039107	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039119	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.90[ASN][1000 genomes]
rs11039122	1.00[YRI][hapmap]
rs11039124	0.87[ASN][1000 genomes]
rs11039134	0.82[ASN][1000 genomes]
rs11600292	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs11600668	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11601798	0.85[CHB][hapmap]
rs11602250	0.84[CHB][hapmap]
rs12224096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12291341	0.83[ASN][1000 genomes]
rs12417519	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs12574410	0.86[CHB][hapmap]
rs12796744	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12807887	0.87[ASN][1000 genomes]
rs17790204	0.82[CHB][hapmap]
rs1872896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1965952	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1976142	0.81[ASN][1000 genomes]
rs1976143	0.83[ASN][1000 genomes]
rs2018527	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2029298	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.83[ASN][1000 genomes]
rs2087215	0.83[CHB][hapmap];0.92[GIH][hapmap]
rs2279438	0.83[CHB][hapmap]
rs2279439	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs2291119	1.00[YRI][hapmap]
rs4237547	0.83[ASN][1000 genomes]
rs4319472	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4394802	0.94[GIH][hapmap];0.83[MEX][hapmap]
rs4528282	0.82[CHB][hapmap]
rs4548577	0.83[CHB][hapmap]
rs4567413	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs4579897	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4581406	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs4587689	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs4752815	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs4752816	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs4752951	0.82[CHB][hapmap]
rs4752952	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4752963	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4752965	0.83[CHB][hapmap]
rs4752967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4752969	0.83[CHB][hapmap];0.92[GIH][hapmap]
rs4752971	0.95[CEU][hapmap];0.87[ASN][1000 genomes]
rs57323109	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6485715	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs6485716	0.86[CHB][hapmap]
rs6485721	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6485722	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6485726	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs6485739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7103581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7108902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7111270	0.83[CHB][hapmap]
rs7111764	0.83[ASN][1000 genomes]
rs7112854	0.82[CHB][hapmap];0.94[GIH][hapmap]
rs7118546	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7119952	0.84[ASN][1000 genomes]
rs7121418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7124648	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs7125807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7126005	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs7128325	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7128650	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs7130006	0.83[CHB][hapmap];0.83[GIH][hapmap]
rs7130947	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs747650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7479189	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs752848	1.00[YRI][hapmap]
rs752850	1.00[YRI][hapmap]
rs7931260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs7935346	0.94[GIH][hapmap]
rs7937101	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.83[ASN][1000 genomes]
rs7937410	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7937950	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938169	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs7940240	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7940441	0.86[GIH][hapmap]
rs7942473	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7945315	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7945558	0.83[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap]
rs7947878	0.87[ASN][1000 genomes]
rs7950753	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs923324	0.82[CHB][hapmap]
rs9633886	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043108	chr11:47041565-47117248	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7946709	F2	cis	cerebellum	SCAN
rs7946709	ACP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47077600-47113200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:47080800-47103000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:47085800-47102400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr11:47089400-47107000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:47089400-47120800	Weak transcription	Hela-S3	cervix
6	chr11:47093600-47101400	Weak transcription	Fetal Intestine Small	intestine
7	chr11:47093800-47103800	Weak transcription	Fetal Intestine Large	intestine
8	chr11:47093800-47105000	Weak transcription	HSMM	muscle
9	chr11:47093800-47105400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr11:47094000-47104000	Weak transcription	Fetal Stomach	stomach
11	chr11:47094000-47105200	Weak transcription	NHEK	skin
12	chr11:47094000-47116400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:47094000-47125200	Weak transcription	Fetal Muscle Leg	muscle
14	chr11:47099800-47101200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr11:47100000-47100800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:47100000-47100800	Enhancers	Osteobl	bone
17	chr11:47100000-47101000	Enhancers	K562	blood
18	chr11:47100200-47101000	Enhancers	Thymus	Thymus
19	chr11:47100200-47103600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:47100400-47100800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr11:47100400-47100800	Enhancers	HSMMtube	muscle
22	chr11:47100400-47101200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:47100600-47100800	Enhancers	NH-A	brain
24	chr11:47100600-47101000	Enhancers	Fetal Lung	lung
25	chr11:47100600-47101000	Enhancers	Fetal Thymus	thymus
26	chr11:47100600-47105200	Weak transcription	NHDF-Ad	bronchial

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