Variant report

Variant	rs6980405
Chromosome Location	chr7:150442625-150442626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:150439063-150443451	GM12892	blood:	n/a	n/a
2	POLR2A	chr7:150442172-150442838	GM12891	blood:	n/a	n/a
3	POLR2A	chr7:150442211-150442699	GM12891	blood:	n/a	n/a
4	POLR2A	chr7:150442010-150442866	GM12892	blood:	n/a	n/a
5	POLR2A	chr7:150440810-150442791	GM12891	blood:	n/a	n/a
6	POLR2A	chr7:150440097-150442944	GM12892	blood:	n/a	n/a
7	POLR2A	chr7:150439308-150443190	GM12892	blood:	n/a	n/a
8	SPI1	chr7:150442358-150442776	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:150434519..150437397-chr7:150442146..150443928,2	K562	blood:

Variant related genes	Relation type
ENSG00000241134	TF binding region
ENSG00000196329	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10239400	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10242011	0.94[ASN][1000 genomes]
rs10271868	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10361	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1046355	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11760839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12703098	0.94[ASN][1000 genomes]
rs17173582	0.82[JPT][hapmap]
rs2286898	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286899	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs28418764	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28505524	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28641865	0.83[ASN][1000 genomes]
rs34078863	0.94[ASN][1000 genomes]
rs34906783	0.93[ASN][1000 genomes]
rs35112724	0.93[ASN][1000 genomes]
rs35257925	0.97[ASN][1000 genomes]
rs4725937	0.94[ASN][1000 genomes]
rs57024360	0.92[ASN][1000 genomes]
rs62490401	0.93[ASN][1000 genomes]
rs62490403	0.93[ASN][1000 genomes]
rs6598	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs759011	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7807580	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9657886	0.81[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9657890	0.95[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9657894	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9657898	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9657900	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9969148	0.93[ASN][1000 genomes]
rs9969242	0.94[ASN][1000 genomes]
rs9969243	0.82[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9969309	0.93[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6980405	RP5-1051J4.4	cis	lung	GTEx
rs6980405	GIMAP8	cis	parietal	SCAN
rs6980405	GIMAP5	cis	Liver	GTEx
rs6980405	RP5-1051J4.4	cis	Adipose Subcutaneous	GTEx
rs6980405	GIMAP5	cis	uninvolved skin	skin_eQTL
rs6980405	RP5-1051J4.4	cis	Whole Blood	GTEx
rs6980405	GIMAP5	cis	normal skin	skin_eQTL
rs6980405	GIMAP5	cis	multi-tissue	Pritchard

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150435400-150442800	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
2	chr7:150436200-150450200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:150436400-150443400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
4	chr7:150436800-150451400	Weak transcription	Brain Substantia Nigra	brain
5	chr7:150437000-150450000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr7:150437200-150443200	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
7	chr7:150437400-150443000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
8	chr7:150437400-150443200	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
9	chr7:150437600-150443200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:150437600-150443800	Weak transcription	Small Intestine	intestine
11	chr7:150438600-150442800	Genic enhancers	Spleen	Spleen
12	chr7:150439800-150443400	Enhancers	Fetal Heart	heart
13	chr7:150440200-150443000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr7:150440400-150446200	Weak transcription	Liver	Liver
15	chr7:150440600-150442800	Genic enhancers	Dnd41	blood
16	chr7:150440600-150443400	Enhancers	Right Ventricle	heart
17	chr7:150440600-150449200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:150441000-150444200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr7:150441000-150445200	Weak transcription	GM12878-XiMat	blood
20	chr7:150441200-150443400	Enhancers	Fetal Muscle Trunk	muscle
21	chr7:150441400-150445400	Weak transcription	Fetal Thymus	thymus
22	chr7:150441400-150449800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:150441600-150443400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:150441600-150447800	Weak transcription	Gastric	stomach
25	chr7:150441600-150450200	Weak transcription	Right Atrium	heart
26	chr7:150442200-150442800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr7:150442200-150442800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
28	chr7:150442200-150443400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr7:150442200-150443400	Enhancers	Fetal Muscle Leg	muscle
30	chr7:150442200-150450000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr7:150442400-150443000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr7:150442400-150443000	Weak transcription	Lung	lung
33	chr7:150442400-150443400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr7:150442400-150449800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr7:150442400-150454600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr7:150442600-150443000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr7:150442600-150443200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr7:150442600-150443200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:150442600-150443400	Enhancers	Fetal Stomach	stomach
40	chr7:150442600-150443400	Enhancers	Left Ventricle	heart
41	chr7:150442600-150449000	Weak transcription	Adipose Nuclei	Adipose

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