Variant report

Variant	rs3913475
Chromosome Location	chr5:75856354-75856355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11948140	0.86[CEU][hapmap];0.91[ASN][1000 genomes]
rs11951829	0.91[ASN][1000 genomes]
rs11952193	0.91[ASN][1000 genomes]
rs11952962	0.86[CEU][hapmap];0.91[ASN][1000 genomes]
rs1393098	0.92[CEU][hapmap];0.91[ASN][1000 genomes]
rs1501689	0.91[ASN][1000 genomes]
rs16873461	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs16873476	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873483	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873519	0.85[CEU][hapmap];0.91[ASN][1000 genomes]
rs2005247	0.91[ASN][1000 genomes]
rs3736395	0.91[ASN][1000 genomes]
rs3913473	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3913474	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703712	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs4704327	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs4704328	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs4704334	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4704335	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704337	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704341	0.92[CEU][hapmap];0.91[ASN][1000 genomes]
rs4704342	0.91[ASN][1000 genomes]
rs4704343	0.91[ASN][1000 genomes]
rs4704344	0.92[CEU][hapmap];0.91[ASN][1000 genomes]
rs58542602	0.89[EUR][1000 genomes]
rs62361989	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62361990	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62361991	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62361992	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62361993	0.93[EUR][1000 genomes]
rs62361994	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62361997	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362011	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362012	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362013	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362014	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362016	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362017	0.95[ASN][1000 genomes]
rs62362019	0.91[ASN][1000 genomes]
rs62362020	0.91[ASN][1000 genomes]
rs62362022	0.91[ASN][1000 genomes]
rs62362035	0.91[ASN][1000 genomes]
rs62362036	0.91[ASN][1000 genomes]
rs62362037	0.91[ASN][1000 genomes]
rs62362038	0.91[ASN][1000 genomes]
rs62362039	0.91[ASN][1000 genomes]
rs62362043	0.91[ASN][1000 genomes]
rs72775801	0.90[EUR][1000 genomes]
rs72777503	0.92[EUR][1000 genomes]
rs72777520	0.91[ASN][1000 genomes]
rs72777522	0.91[ASN][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
rs3913475	IQGAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 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	chr5:75843800-75884400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:75844400-75860400	Weak transcription	Placenta	Placenta
4	chr5:75844800-75857200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr5:75844800-75857400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr5:75845000-75856400	Weak transcription	Liver	Liver
7	chr5:75845000-75858200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:75845400-75876600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr5:75845600-75857200	Weak transcription	Gastric	stomach
10	chr5:75846800-75902600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:75848600-75857000	Weak transcription	Stomach Mucosa	stomach
12	chr5:75849800-75857200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:75851600-75861200	Weak transcription	Thymus	Thymus
14	chr5:75851800-75857200	Weak transcription	Esophagus	oesophagus
15	chr5:75851800-75858000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr5:75851800-75860200	Weak transcription	HepG2	liver
17	chr5:75851800-75892000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr5:75852000-75864400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:75852600-75857000	Weak transcription	K562	blood
20	chr5:75852800-75857600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr5:75852800-75858400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:75852800-75860400	Weak transcription	Fetal Intestine Small	intestine
23	chr5:75852800-75877800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr5:75852800-75877800	Weak transcription	Small Intestine	intestine
25	chr5:75853000-75856600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr5:75853000-75857200	Weak transcription	Pancreas	Pancrea
27	chr5:75853000-75857400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr5:75853000-75858400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr5:75853000-75858400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:75853200-75857600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:75853200-75896400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr5:75853400-75857200	Weak transcription	GM12878-XiMat	blood
33	chr5:75853400-75858000	Weak transcription	Primary B cells from cord blood	blood
34	chr5:75853400-75858600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:75854600-75863000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr5:75854800-75858800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:75855400-75859000	Strong transcription	Primary T cells from cord blood	blood
38	chr5:75855800-75857200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr5:75855800-75857200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:75855800-75857400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:75855800-75862400	Weak transcription	Fetal Thymus	thymus
42	chr5:75856000-75856800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr5:75856000-75857000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr5:75856200-75859800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr5:75856200-75860200	Weak transcription	Fetal Stomach	stomach

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