Variant report

Variant	rs6944166
Chromosome Location	chr7:40259553-40259554
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10081308	0.84[ASN][1000 genomes]
rs10081355	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10227386	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10228020	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10229517	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10230530	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10234693	0.81[CEU][hapmap]
rs10242519	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10243494	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10246466	0.80[CEU][hapmap]
rs10259565	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10261251	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10267954	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10269349	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10272641	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs10275761	0.81[CEU][hapmap]
rs10276687	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10951626	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10951627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11760739	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11763047	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11767697	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11768838	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11769327	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12333691	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12333929	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12530776	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12534074	0.82[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs12535524	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13231777	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13233333	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1406565	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1406566	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1534675	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17171658	0.82[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs1830422	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1874232	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1874233	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1881683	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1881684	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1919615	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1973398	0.90[CEU][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1989589	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2009560	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2019838	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024200	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036041	0.92[CEU][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2052097	0.81[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs2056775	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2109340	0.87[ASN][1000 genomes]
rs2329695	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28733232	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28742222	0.88[ASN][1000 genomes]
rs34960564	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs388354	0.85[ASN][1000 genomes]
rs3966459	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4720354	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4723931	0.85[ASN][1000 genomes]
rs4723934	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60008412	0.82[EUR][1000 genomes]
rs6462961	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6462962	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6462963	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6462965	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];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66481381	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66912039	0.89[ASN][1000 genomes]
rs67438499	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6948982	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6951375	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6952597	0.83[MEX][hapmap];0.82[TSI][hapmap]
rs6954096	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6957274	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6957766	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6962410	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6963804	0.88[ASN][1000 genomes]
rs6968402	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6974493	0.88[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs6978474	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6979628	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71560176	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs731847	0.81[CEU][hapmap]
rs731848	0.83[MEX][hapmap]
rs773402	0.81[CEU][hapmap]
rs7776964	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7776967	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7778061	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7779560	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7780858	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7796371	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7797041	0.81[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs7802584	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7808529	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7809368	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7810509	0.88[ASN][1000 genomes]
rs887445	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs887447	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9639824	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9690188	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9791485	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756801	chr7:40060180-40269583	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic 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	17 gene(s)	inside rSNPs	diseases
2	esv2759525	chr7:40060180-40269583	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1032278	chr7:40097371-40396300	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv464438	chr7:40193535-40350887	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv606710	chr7:40193535-40350887	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1019032	chr7:40204606-40280323	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv887983	chr7:40211563-40284166	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv606711	chr7:40225129-40360257	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv887984	chr7:40227307-40284166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6944166	CDC2L5	Cis_1M	lymphoblastoid	RTeQTL
rs6944166	C7orf36	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40221600-40259800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr7:40236600-40264400	Weak transcription	Pancreas	Pancrea
3	chr7:40240400-40260800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:40242800-40259800	Weak transcription	Ovary	ovary
5	chr7:40251400-40264200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:40253200-40264000	Weak transcription	Aorta	Aorta
7	chr7:40256600-40259600	Weak transcription	HepG2	liver
8	chr7:40258200-40263400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:40258200-40264000	Weak transcription	Liver	Liver
10	chr7:40258600-40260600	Genic enhancers	HSMM	muscle
11	chr7:40258600-40262400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:40258800-40259800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr7:40258800-40263200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr7:40258800-40271800	Weak transcription	Fetal Intestine Large	intestine
15	chr7:40258800-40273800	Weak transcription	Fetal Intestine Small	intestine
16	chr7:40259000-40260600	Enhancers	HSMMtube	muscle
17	chr7:40259000-40260600	Enhancers	NHDF-Ad	bronchial
18	chr7:40259000-40261600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr7:40259000-40262600	Enhancers	Osteobl	bone
20	chr7:40259000-40262800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr7:40259000-40263400	Enhancers	HMEC	breast
22	chr7:40259000-40264200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr7:40259200-40259600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr7:40259200-40262200	Enhancers	HUVEC	blood vessel
25	chr7:40259200-40262600	Enhancers	NH-A	brain
26	chr7:40259200-40263400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:40259200-40263400	Enhancers	NHEK	skin
28	chr7:40259200-40263600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:40259400-40262000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr7:40259400-40262200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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