Variant report

Variant	rs62362016
Chromosome Location	chr5:75882513-75882514
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11948140	0.91[ASN][1000 genomes]
rs11951829	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11952193	0.91[ASN][1000 genomes]
rs11952962	0.91[ASN][1000 genomes]
rs1393098	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1501689	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16873476	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873483	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873519	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2005247	0.91[ASN][1000 genomes]
rs3736395	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3913473	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3913474	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3913475	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704328	0.84[EUR][1000 genomes]
rs4704334	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4704335	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704337	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704339	0.84[AFR][1000 genomes]
rs4704341	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4704342	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4704343	0.91[ASN][1000 genomes]
rs4704344	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58542602	0.84[EUR][1000 genomes]
rs62361989	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62361990	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62361991	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62361992	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62361993	0.89[EUR][1000 genomes]
rs62361994	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62361997	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362011	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362012	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362013	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362014	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362017	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62362019	0.91[ASN][1000 genomes]
rs62362020	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62362022	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62362035	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62362036	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62362037	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62362038	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62362039	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62362043	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72775801	0.86[EUR][1000 genomes]
rs72777503	0.88[EUR][1000 genomes]
rs72777520	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72777522	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv598681	chr5:75863987-75902533	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	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
rs62362016	IQGAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75843800-75884400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:75846800-75902600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:75851800-75892000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:75853200-75896400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr5:75861200-75889600	Weak transcription	Fetal Stomach	stomach
6	chr5:75862200-75885400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:75865400-75885800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:75867800-75886000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr5:75868000-75884400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:75868000-75885200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:75868000-75885400	Weak transcription	Primary T cells from cord blood	blood
12	chr5:75873600-75903600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:75874000-75892400	Weak transcription	Spleen	Spleen
14	chr5:75875200-75884000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr5:75877000-75885200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:75877000-75902800	Weak transcription	Adipose Nuclei	Adipose
17	chr5:75877400-75902800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:75879000-75885000	Weak transcription	Placenta	Placenta
19	chr5:75879000-75892400	Weak transcription	Pancreas	Pancrea
20	chr5:75879000-75913600	Weak transcription	Colonic Mucosa	Colon
21	chr5:75879000-75917600	Weak transcription	Fetal Thymus	thymus
22	chr5:75879000-75934000	Weak transcription	Small Intestine	intestine
23	chr5:75879200-75883400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr5:75879200-75885000	Weak transcription	Primary B cells from cord blood	blood
25	chr5:75879200-75885200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr5:75879200-75885400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr5:75879200-75885400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr5:75879200-75888600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr5:75879200-75888800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr5:75879200-75900600	Weak transcription	Fetal Intestine Small	intestine
31	chr5:75879200-75907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:75879200-75919000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr5:75879400-75885400	Weak transcription	Liver	Liver
34	chr5:75879400-75903400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr5:75879600-75882800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:75879600-75886800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr5:75879600-75888600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:75880200-75882800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr5:75880200-75882800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:75880200-75883000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr5:75880200-75883000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:75880200-75933400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr5:75880600-75892600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr5:75880800-75887400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:75880800-75897600	Weak transcription	HepG2	liver
46	chr5:75881800-75884000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr5:75882000-75885000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr5:75882000-75901400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:75882200-75882600	Enhancers	Stomach Mucosa	stomach
50	chr5:75882400-75882800	Enhancers	Gastric	stomach

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