Variant report

Variant	rs2140595
Chromosome Location	chr7:150163837-150163838
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1113485	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11769211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1608627	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2373748	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2373749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146035	0.85[GIH][hapmap];0.80[MEX][hapmap]
rs56693569	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58111571	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59777480	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60114833	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61342202	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6464067	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6947973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6969414	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73155823	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73155829	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1025129	chr7:150146593-150266217	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2140595	DPP6	cis	parietal	SCAN
rs2140595	GIMAP8	cis	Adipose Subcutaneous	GTEx
rs2140595	GIMAP8	cis	Muscle Skeletal	GTEx
rs2140595	GIMAP8	cis	Nerve Tibial	GTEx
rs2140595	ZNF425	cis	cerebellum	SCAN
rs2140595	GIMAP8	cis	Skin Sun Exposed Lower leg	GTEx
rs2140595	GIMAP8	Cis_1M	lymphoblastoid	RTeQTL
rs2140595	GIMAP4	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150158000-150168000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:150158400-150174200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:150160400-150166200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
4	chr7:150160600-150165000	Genic enhancers	Primary T cells from cord blood	blood
5	chr7:150160600-150168400	Genic enhancers	Primary monocytes fromperipheralblood	blood
6	chr7:150161200-150175200	Weak transcription	Small Intestine	intestine
7	chr7:150161200-150178400	Weak transcription	Esophagus	oesophagus
8	chr7:150162200-150164200	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr7:150162200-150176600	Weak transcription	Colonic Mucosa	Colon
10	chr7:150162400-150164000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:150162600-150164400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr7:150162800-150164600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:150162800-150171000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr7:150163000-150164000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr7:150163000-150164400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr7:150163000-150166800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:150163000-150166800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:150163000-150167800	Active TSS	Right Atrium	heart
19	chr7:150163200-150164000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr7:150163200-150164000	Enhancers	Brain Substantia Nigra	brain
21	chr7:150163200-150164000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr7:150163200-150164200	Enhancers	Brain Hippocampus Middle	brain
23	chr7:150163400-150165200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr7:150163400-150171400	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr7:150163600-150164000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:150163600-150164200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:150163600-150164200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:150163600-150164200	Flanking Active TSS	NHEK	skin
29	chr7:150163600-150164400	Transcr. at gene 5' and 3'	HUVEC	blood vessel
30	chr7:150163600-150164600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr7:150163600-150166000	Active TSS	Right Ventricle	heart
32	chr7:150163600-150166600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr7:150163600-150166600	Active TSS	Psoas Muscle	Psoas
34	chr7:150163600-150176600	Weak transcription	Primary B cells from cord blood	blood
35	chr7:150163800-150164000	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr7:150163800-150164000	Genic enhancers	GM12878-XiMat	blood
37	chr7:150163800-150164000	Bivalent Enhancer	HepG2	liver
38	chr7:150163800-150164200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
39	chr7:150163800-150164200	Enhancers	Brain Anterior Caudate	brain
40	chr7:150163800-150164200	Enhancers	Brain Cingulate Gyrus	brain
41	chr7:150163800-150164200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr7:150163800-150164200	Enhancers	Gastric	stomach
43	chr7:150163800-150164200	Transcr. at gene 5' and 3'	Lung	lung
44	chr7:150163800-150164200	Genic enhancers	Monocytes-CD14+_RO01746	blood
45	chr7:150163800-150164400	Strong transcription	Liver	Liver
46	chr7:150163800-150164400	Transcr. at gene 5' and 3'	Left Ventricle	heart
47	chr7:150163800-150164400	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr7:150163800-150164400	Flanking Active TSS	HMEC	breast
49	chr7:150163800-150164600	Strong transcription	Primary hematopoietic stem cells	blood
50	chr7:150163800-150164800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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