Variant report

Variant	rs9969243
Chromosome Location	chr7:150446692-150446693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10239400	0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10242011	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10271868	0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10361	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1046355	0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11760839	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12703098	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17173582	0.82[JPT][hapmap]
rs2286898	0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2286899	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28418764	0.93[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28505524	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28641865	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34078863	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34906783	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35112724	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35257925	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4725937	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57024360	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62490401	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62490403	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6598	0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6980405	0.82[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs759011	0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7807580	0.95[ASN][1000 genomes]
rs9657886	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9657890	0.94[JPT][hapmap]
rs9657894	0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9657898	0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9657900	0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9969148	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9969242	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9969309	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
8	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
9	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9969243	GIMAP5	cis	multi-tissue	Pritchard
rs9969243	LR8	cis	multi-tissue	Pritchard
rs9969243	GIMAP5	cis	lymphoblastoid	seeQTL
rs9969243	LRRC61	cis	parietal	SCAN
rs9969243	HCA112	cis	multi-tissue	Pritchard

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150436200-150450200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr7:150436800-150451400	Weak transcription	Brain Substantia Nigra	brain
3	chr7:150437000-150450000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:150440600-150449200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:150441400-150449800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:150441600-150447800	Weak transcription	Gastric	stomach
7	chr7:150441600-150450200	Weak transcription	Right Atrium	heart
8	chr7:150442200-150450000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr7:150442400-150449800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr7:150442400-150454600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr7:150442600-150449000	Weak transcription	Adipose Nuclei	Adipose
12	chr7:150442800-150450000	Weak transcription	Dnd41	blood
13	chr7:150443000-150452200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr7:150443200-150447200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr7:150443200-150450000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:150443200-150451200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr7:150443200-150452200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:150443200-150452400	Weak transcription	Spleen	Spleen
19	chr7:150443400-150449200	Weak transcription	Left Ventricle	heart
20	chr7:150443400-150449400	Weak transcription	Right Ventricle	heart
21	chr7:150444000-150447200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr7:150444200-150447000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr7:150444600-150452200	Enhancers	Primary T cells from cord blood	blood
24	chr7:150444800-150448200	Enhancers	Primary T cells fromperipheralblood	blood
25	chr7:150445400-150452000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr7:150445600-150452200	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr7:150445800-150450000	Weak transcription	Fetal Thymus	thymus
28	chr7:150446000-150450200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr7:150446200-150448200	Enhancers	Liver	Liver
30	chr7:150446200-150450000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:150446200-150451400	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr7:150446200-150452200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr7:150446400-150447000	Enhancers	Fetal Heart	heart
34	chr7:150446400-150449000	Weak transcription	GM12878-XiMat	blood
35	chr7:150446600-150450000	Enhancers	Primary T helper cells PMA-I stimulated	--

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