Variant report

Variant	rs11952193
Chromosome Location	chr5:75895252-75895253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11948140	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951829	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952962	1.00[CHB][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393098	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1501689	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873476	0.91[ASN][1000 genomes]
rs16873483	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16873519	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005247	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736395	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3913473	0.91[ASN][1000 genomes]
rs3913474	0.91[ASN][1000 genomes]
rs3913475	0.91[ASN][1000 genomes]
rs4704335	0.91[ASN][1000 genomes]
rs4704337	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4704341	1.00[CHB][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704344	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62361989	0.91[ASN][1000 genomes]
rs62361990	0.83[ASN][1000 genomes]
rs62361991	0.91[ASN][1000 genomes]
rs62361992	0.83[ASN][1000 genomes]
rs62361997	0.91[ASN][1000 genomes]
rs62362011	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62362012	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62362013	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62362014	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62362016	0.91[ASN][1000 genomes]
rs62362017	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62362019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362020	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362022	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362035	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362036	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362037	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362038	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362039	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62362042	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62362043	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72777520	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72777522	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs11952193	IQGAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75846800-75902600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:75853200-75896400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr5:75873600-75903600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:75877000-75902800	Weak transcription	Adipose Nuclei	Adipose
5	chr5:75877400-75902800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:75879000-75913600	Weak transcription	Colonic Mucosa	Colon
7	chr5:75879000-75917600	Weak transcription	Fetal Thymus	thymus
8	chr5:75879000-75934000	Weak transcription	Small Intestine	intestine
9	chr5:75879200-75900600	Weak transcription	Fetal Intestine Small	intestine
10	chr5:75879200-75907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:75879200-75919000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:75879400-75903400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:75880200-75933400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr5:75880800-75897600	Weak transcription	HepG2	liver
15	chr5:75882000-75901400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:75882600-75969400	Weak transcription	Stomach Mucosa	stomach
17	chr5:75883400-75904200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr5:75884000-75903000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr5:75884000-75914600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr5:75884200-75902200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:75884400-75919200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr5:75884400-75919400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr5:75885200-75900800	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr5:75885400-75905000	Strong transcription	Primary hematopoietic stem cells	blood
25	chr5:75886200-75902800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:75886400-75898600	Weak transcription	GM12878-XiMat	blood
27	chr5:75889400-75903000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr5:75889400-75903000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr5:75889800-75896200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr5:75891000-75911800	Weak transcription	Thymus	Thymus
31	chr5:75891200-75909200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:75891200-75911800	Strong transcription	Liver	Liver
33	chr5:75892000-75899200	Strong transcription	Placenta	Placenta
34	chr5:75892000-75902400	Strong transcription	Primary B cells from cord blood	blood
35	chr5:75892000-75904000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:75892000-75910400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr5:75892200-75895600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr5:75892800-75896600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr5:75893400-75897800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr5:75893400-75902000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr5:75893400-75903400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr5:75893400-75903400	Weak transcription	Spleen	Spleen
43	chr5:75893600-75896200	Weak transcription	Primary T cells from cord blood	blood
44	chr5:75893600-75896200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr5:75893600-75896200	Weak transcription	Pancreas	Pancrea
46	chr5:75893600-75896600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr5:75893600-75898600	Weak transcription	Fetal Stomach	stomach
48	chr5:75893600-75898800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr5:75893600-75902600	Weak transcription	Gastric	stomach
50	chr5:75893600-75903200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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