Variant report

Variant	rs1403220
Chromosome Location	chr7:150363700-150363701
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:150359279..150361425-chr7:150361941..150364354,2	K562	blood:
2	chr7:150362686..150366061-chr7:150367736..150370003,3	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10254829	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs11769703	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12154435	0.96[ASN][1000 genomes]
rs12154436	0.96[ASN][1000 genomes]
rs12154687	0.85[ASN][1000 genomes]
rs1234356	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1234357	0.87[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1234361	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12397707	0.84[ASN][1000 genomes]
rs12532045	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535208	0.85[ASN][1000 genomes]
rs12537789	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs12703091	0.86[ASN][1000 genomes]
rs1316352	0.96[ASN][1000 genomes]
rs13220967	0.85[ASN][1000 genomes]
rs13225905	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13226190	0.90[ASN][1000 genomes]
rs13230583	0.86[ASN][1000 genomes]
rs13234724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13238412	0.86[ASN][1000 genomes]
rs13240099	0.85[ASN][1000 genomes]
rs13240106	0.85[ASN][1000 genomes]
rs17542143	0.90[ASN][1000 genomes]
rs34030180	0.95[ASN][1000 genomes]
rs34396063	0.96[ASN][1000 genomes]
rs34585329	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34940374	0.92[ASN][1000 genomes]
rs35283918	0.91[ASN][1000 genomes]
rs35285840	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35329030	0.96[ASN][1000 genomes]
rs35342751	0.86[ASN][1000 genomes]
rs35760614	0.91[ASN][1000 genomes]
rs36020504	0.96[ASN][1000 genomes]
rs36065681	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735080	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs3735086	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3807382	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs56138121	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56279394	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56325059	0.86[ASN][1000 genomes]
rs56412316	0.96[ASN][1000 genomes]
rs59468128	0.95[ASN][1000 genomes]
rs62490361	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62490366	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62491810	0.86[ASN][1000 genomes]
rs62491812	0.90[ASN][1000 genomes]
rs62491814	0.92[ASN][1000 genomes]
rs62491829	0.96[ASN][1000 genomes]
rs73474862	0.96[ASN][1000 genomes]
rs7784050	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7808446	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs954395	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	esv2758617	chr7:150251949-150463804	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2759573	chr7:150251949-150463804	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv3388935	chr7:150301204-150374532	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv831187	chr7:150325913-150503500	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1403220	GIMAP4	Cis_1M	lymphoblastoid	RTeQTL
rs1403220	ATP6V0E2	cis	cerebellum	SCAN
rs1403220	GIMAP2	cis	parietal	SCAN
rs1403220	ZNF282	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150357600-150365000	Enhancers	Primary T cells from cord blood	blood
2	chr7:150358000-150365400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr7:150358000-150369000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr7:150358600-150365600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr7:150359400-150366400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:150360400-150365400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr7:150360400-150367000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr7:150360600-150367000	Enhancers	Fetal Thymus	thymus
9	chr7:150360800-150363800	Enhancers	Spleen	Spleen
10	chr7:150360800-150364400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr7:150361200-150364600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr7:150361200-150365600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:150361200-150366000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr7:150361600-150365000	Weak transcription	Primary B cells from cord blood	blood
15	chr7:150361600-150365400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr7:150361600-150366000	Enhancers	GM12878-XiMat	blood
17	chr7:150362200-150365600	Enhancers	Thymus	Thymus
18	chr7:150362600-150363800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:150362600-150364000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr7:150362600-150366200	Enhancers	Primary hematopoietic stem cells	blood
21	chr7:150362800-150363800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:150362800-150364000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr7:150362800-150368000	Weak transcription	Right Atrium	heart
24	chr7:150363200-150364800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr7:150363400-150367800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:150363600-150363800	Flanking Active TSS	Dnd41	blood
27	chr7:150363600-150364000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr7:150363600-150364400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr7:150363600-150364600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr7:150363600-150365000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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