Variant report

Variant	rs62361994
Chromosome Location	chr5:75851484-75851485
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs16873461	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16873476	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16873483	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3913473	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3913474	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3913475	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4704327	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4704328	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4704334	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704335	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4704337	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58542602	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62361989	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62361990	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62361991	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62361992	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62361993	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62361997	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62362011	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62362012	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62362013	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62362014	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62362016	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62362017	0.81[ASN][1000 genomes]
rs72775801	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72777503	0.95[AMR][1000 genomes];0.97[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
rs62361994	IQGAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75835600-75871200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:75842600-75851600	Weak transcription	Esophagus	oesophagus
3	chr5:75843800-75884400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:75844200-75854000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:75844200-75854400	Weak transcription	Fetal Stomach	stomach
6	chr5:75844200-75855400	Weak transcription	Primary T cells from cord blood	blood
7	chr5:75844400-75852200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr5:75844400-75852200	Weak transcription	Primary B cells from cord blood	blood
9	chr5:75844400-75860400	Weak transcription	Placenta	Placenta
10	chr5:75844800-75857200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:75844800-75857400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:75845000-75852800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:75845000-75856400	Weak transcription	Liver	Liver
14	chr5:75845000-75858200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:75845400-75876600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr5:75845600-75857200	Weak transcription	Gastric	stomach
17	chr5:75845800-75852400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:75846200-75852600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr5:75846800-75902600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:75848600-75857000	Weak transcription	Stomach Mucosa	stomach
21	chr5:75849000-75851800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:75849800-75852200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:75849800-75857200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:75850400-75852600	Enhancers	GM12878-XiMat	blood
25	chr5:75850400-75853200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr5:75850800-75851800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr5:75851000-75853000	Enhancers	Primary hematopoietic stem cells	blood
28	chr5:75851200-75851600	Enhancers	Primary T cells fromperipheralblood	blood
29	chr5:75851200-75851800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr5:75851200-75851800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr5:75851200-75851800	Enhancers	Pancreas	Pancrea
32	chr5:75851200-75852000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr5:75851200-75852400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr5:75851200-75852400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:75851200-75853000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr5:75851200-75853200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:75851400-75851800	Strong transcription	HepG2	liver
38	chr5:75851400-75852200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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