Variant report

Variant	rs62362042
Chromosome Location	chr5:75906070-75906071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11948140	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11951829	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11952193	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11952962	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1393098	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1501689	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16873519	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2005247	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3736395	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4704341	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4704342	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4704343	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4704344	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62362012	0.80[EUR][1000 genomes]
rs62362013	0.84[EUR][1000 genomes]
rs62362017	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62362019	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62362020	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62362022	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62362035	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62362036	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62362037	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62362038	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62362039	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62362043	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72777520	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72777522	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022032	chr5:75785106-75914003	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv598679	chr5:75823965-75914729	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1023953	chr5:75831037-75913784	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026257	chr5:75831037-75914003	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	2 gene(s)	inside rSNPs	diseases
5	nsv1016823	chr5:75831037-75915905	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv598680	chr5:75839165-75914729	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62362042	IQGAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75879000-75913600	Weak transcription	Colonic Mucosa	Colon
2	chr5:75879000-75917600	Weak transcription	Fetal Thymus	thymus
3	chr5:75879000-75934000	Weak transcription	Small Intestine	intestine
4	chr5:75879200-75907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:75879200-75919000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:75880200-75933400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr5:75882600-75969400	Weak transcription	Stomach Mucosa	stomach
8	chr5:75884000-75914600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr5:75884400-75919200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr5:75884400-75919400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr5:75891000-75911800	Weak transcription	Thymus	Thymus
12	chr5:75891200-75909200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:75891200-75911800	Strong transcription	Liver	Liver
14	chr5:75892000-75910400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr5:75895200-75912800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr5:75896800-75913800	Weak transcription	Pancreas	Pancrea
17	chr5:75898000-75908800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:75899600-75907200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr5:75900800-75907400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr5:75901000-75906800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr5:75901200-75911200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr5:75901200-75917000	Weak transcription	HUVEC	blood vessel
23	chr5:75901400-75912400	Weak transcription	Fetal Intestine Large	intestine
24	chr5:75901600-75907600	Weak transcription	Fetal Intestine Small	intestine
25	chr5:75902600-75919200	Strong transcription	Primary T cells from cord blood	blood
26	chr5:75903000-75906800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr5:75903000-75907200	Weak transcription	GM12878-XiMat	blood
28	chr5:75903400-75908800	Weak transcription	Gastric	stomach
29	chr5:75903600-75914800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr5:75903600-75917800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:75903800-75906200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:75903800-75906800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr5:75903800-75907200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr5:75903800-75907200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:75903800-75907400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr5:75903800-75910000	Weak transcription	Osteobl	bone
37	chr5:75903800-75910600	Weak transcription	Ovary	ovary
38	chr5:75903800-75910800	Weak transcription	NHDF-Ad	bronchial
39	chr5:75903800-75913200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:75903800-75914400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr5:75903800-75916000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr5:75903800-75916000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr5:75903800-75917800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr5:75903800-75918800	Weak transcription	Fetal Kidney	kidney
45	chr5:75903800-75918800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr5:75903800-75936200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:75903800-75943600	Weak transcription	Spleen	Spleen
48	chr5:75904000-75906800	Weak transcription	HepG2	liver
49	chr5:75904000-75907000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:75904000-75911400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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