Variant report

Variant	rs7588883
Chromosome Location	chr2:32397267-32397268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:32395858..32398697-chr2:32406981..32409057,2	K562	blood:
2	chr2:32397197..32398862-chr2:32406291..32408481,2	K562	blood:
3	chr2:32394949..32397744-chr2:32404684..32406566,2	MCF-7	breast:

Extended variants
information (count: 115 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10172468	0.84[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10208246	0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10490360	0.95[CHB][hapmap]
rs11124274	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap]
rs11124275	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs11124278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11676475	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11676938	0.95[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap]
rs11678119	0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.89[ASN][1000 genomes]
rs11683760	0.81[ASN][1000 genomes]
rs11683842	0.81[ASN][1000 genomes]
rs11694630	0.89[ASN][1000 genomes]
rs12465124	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12465351	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12474598	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12614686	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12989936	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.81[MKK][hapmap]
rs12995952	0.86[ASN][1000 genomes]
rs12997026	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13017189	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap]
rs13022197	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs13427170	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431540	0.80[AMR][1000 genomes]
rs177083	0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs17767988	0.95[CHB][hapmap]
rs212679	0.91[JPT][hapmap]
rs212686	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs212687	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs212694	0.89[EUR][1000 genomes]
rs212703	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs212704	0.96[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs212706	0.83[CEU][hapmap]
rs212707	0.83[CEU][hapmap]
rs212708	0.83[CEU][hapmap];0.85[YRI][hapmap]
rs212713	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.90[EUR][1000 genomes]
rs212715	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs212716	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap]
rs212717	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap]
rs212738	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs212739	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs212740	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs212741	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs212743	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs212744	1.00[CEU][hapmap];0.91[JPT][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs212745	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs212746	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs212748	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs212749	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs212752	0.81[EUR][1000 genomes]
rs212753	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs212755	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs212757	0.93[EUR][1000 genomes]
rs212760	0.91[JPT][hapmap]
rs212762	0.95[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs216544	0.83[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2280967	0.95[CHB][hapmap];0.97[CHD][hapmap];0.80[LWK][hapmap]
rs2280973	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2365555	0.95[CHB][hapmap];0.97[CHD][hapmap]
rs2366736	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2886393	0.84[ASN][1000 genomes]
rs34976640	0.84[ASN][1000 genomes]
rs3752916	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs3752917	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3769602	0.90[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.89[ASN][1000 genomes]
rs3769603	0.82[ASN][1000 genomes]
rs3769604	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap]
rs3769606	0.95[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs3851308	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3851310	0.80[ASN][1000 genomes]
rs4258846	0.96[ASN][1000 genomes]
rs435572	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap]
rs4407291	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs443609	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs4519572	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs467523	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs479333	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs4952209	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4952248	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4952250	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4952252	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55877106	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56208031	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62134021	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs659239	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap]
rs6716179	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6717209	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6723154	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs6725184	0.82[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap]
rs6737500	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs6748621	0.85[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap]
rs6752375	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs6758024	0.95[CHB][hapmap]
rs6760105	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap]
rs6761417	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72863940	0.81[AMR][1000 genomes]
rs7561519	0.91[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap]
rs7566162	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7572964	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7573543	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7577696	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap]
rs7581340	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs7581432	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7586448	0.95[CHB][hapmap]
rs7592239	0.86[ASN][1000 genomes]
rs7592356	0.83[ASN][1000 genomes]
rs7601267	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap]
rs7604289	0.82[ASN][1000 genomes]
rs7605242	0.95[CHB][hapmap];0.86[JPT][hapmap]

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	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv873778	chr2:32297984-32409007	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised 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	39 gene(s)	inside rSNPs	diseases
5	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7588883	NLRC4	cis	Lymphoblastoid	GTEx
rs7588883	EHD3	cis	parietal	SCAN
rs7588883	NLRC4	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32391400-32401800	Weak transcription	Spleen	Spleen
2	chr2:32391400-32402000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:32391400-32402000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:32391600-32397400	Weak transcription	Left Ventricle	heart
5	chr2:32391600-32401800	Weak transcription	Gastric	stomach
6	chr2:32391600-32402000	Weak transcription	Esophagus	oesophagus
7	chr2:32391600-32402800	Weak transcription	Lung	lung
8	chr2:32391600-32403400	Weak transcription	Aorta	Aorta
9	chr2:32391600-32406600	Weak transcription	Small Intestine	intestine
10	chr2:32391600-32409600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:32391600-32426400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:32391600-32452800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:32391800-32397600	Weak transcription	Fetal Thymus	thymus
14	chr2:32391800-32397600	Weak transcription	Ovary	ovary
15	chr2:32391800-32397800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:32391800-32400200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:32391800-32400200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr2:32391800-32401800	Weak transcription	Brain Substantia Nigra	brain
19	chr2:32391800-32409600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:32391800-32431400	Weak transcription	Stomach Mucosa	stomach
21	chr2:32391800-32453800	Weak transcription	Colonic Mucosa	Colon
22	chr2:32392000-32397400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:32392000-32397600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:32392000-32397600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:32392000-32397600	Weak transcription	HMEC	breast
26	chr2:32392000-32397800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:32392000-32397800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:32392000-32398200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:32392000-32401800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:32392000-32401800	Weak transcription	Brain Angular Gyrus	brain
31	chr2:32392000-32401800	Weak transcription	Fetal Stomach	stomach
32	chr2:32392000-32402000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:32392000-32402000	Weak transcription	Fetal Lung	lung
34	chr2:32392000-32402000	Weak transcription	Thymus	Thymus
35	chr2:32392000-32402200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr2:32392000-32403600	Weak transcription	Fetal Kidney	kidney
37	chr2:32392000-32403800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:32392000-32403800	Weak transcription	HSMMtube	muscle
39	chr2:32392000-32414600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:32392000-32435800	Weak transcription	NHLF	lung
41	chr2:32392200-32397400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:32392200-32397400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:32392200-32397400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr2:32392200-32397400	Weak transcription	NHEK	skin
45	chr2:32392200-32397600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr2:32392200-32398400	Weak transcription	Fetal Intestine Small	intestine
47	chr2:32392200-32402000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr2:32392200-32402000	Weak transcription	Brain Germinal Matrix	brain
49	chr2:32392200-32402200	Weak transcription	Osteobl	bone
50	chr2:32392200-32403600	Weak transcription	HUVEC	blood vessel

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