Variant report

Variant	rs2286900
Chromosome Location	chr7:150418045-150418046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:150418017-150418067	NB4	blood:	n/a
2	chr7:150418017-150418067	U87	brain:	n/a
3	chr7:150418017-150418067	AG10803	skin:	n/a
4	chr7:150418017-150418067	PrEC	prostate:	n/a
5	chr7:150418017-150418067	SK-N-MC	brain:	n/a
6	chr7:150418017-150418067	HMEC	breast:	n/a
7	chr7:150418017-150418067	SAEC	small airway:	n/a
8	chr7:150418017-150418067	AG04450	lung:	fetal
9	chr7:150418017-150418067	BE2_C	brain:	n/a
10	chr7:150418017-150418067	BJ	skin:	n/a
11	chr7:150418017-150418067	HepG2	liver:	n/a
12	chr7:150418017-150418067	K562	blood:	n/a
13	chr7:150418017-150418067	HUVEC	blood vessel:	n/a
14	chr7:150418017-150418067	MCF10A-Er-Src	breast:	n/a
15	chr7:150418017-150418067	HPAEpiC	pulmonary alveolar:	n/a
16	chr7:150418017-150418067	GM12892	blood:	n/a
17	chr7:150418017-150418067	RPTEC	kidney:	n/a
18	chr7:150418017-150418067	AG09319	gingival:	n/a
19	chr7:150418017-150418067	SKMC	muscle:	n/a
20	chr7:150418017-150418067	HCT-116	colon:	n/a
21	chr7:150418017-150418067	Hela-S3	cervix:	n/a
22	chr7:150418017-150418067	HRE	kidney:	n/a
23	chr7:150418017-150418067	Caco-2	colon:	n/a
24	chr7:150418017-150418067	HCF	heart:	n/a
25	chr7:150418017-150418067	MCF-7	breast:	n/a
26	chr7:150418017-150418067	NHBE	bronchial:	n/a
27	chr7:150418017-150418067	HCM	heart:	n/a
28	chr7:150418017-150418067	GM06990	blood:	n/a
29	chr7:150418017-150418067	PFSK-1	brain:	n/a
30	chr7:150418017-150418067	HRPEpiC	eye:	n/a
31	chr7:150418017-150418067	SK-N-SH	brain:	n/a
32	chr7:150418017-150418067	HL-60	blood:	n/a
33	chr7:150418017-150418067	HEK293	kidney:	embryo
34	chr7:150418017-150418067	ProgFib	skin:	n/a
35	chr7:150418017-150418067	HEEpiC	esophagus:	n/a
36	chr7:150418017-150418067	HNPCEpiC	eye:	n/a
37	chr7:150418017-150418067	A549	lung:	n/a
38	chr7:150418017-150418067	AG04449	skin:	fetal
39	chr7:150418017-150418067	AoSMC	blood vessel:	n/a
40	chr7:150418017-150418067	NHDF-neo	bronchial:	n/a
41	chr7:150418017-150418067	T-47D	breast:	n/a
42	chr7:150418017-150418067	ECC-1	luminal epithelium:	n/a
43	chr7:150418017-150418067	HIPEpiC	eye:	n/a
44	chr7:150418017-150418067	NH-A	brain:	n/a
45	chr7:150418017-150418067	NT2-D1	testis:	n/a
46	chr7:150418017-150418067	HRCEpiC	kidney:	n/a
47	chr7:150418017-150418067	GM12878	blood:	n/a
48	chr7:150418017-150418067	H1-hESC	embryonic stem cell:	embryo
49	chr7:150418017-150418067	IMR90	lung:	fetal
50	chr7:150418017-150418067	ovcar-3	ovarian:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:150411749..150416479-chr7:150417256..150421069,5	K562	blood:
2	chr7:150417526..150419124-chr7:150425522..150427293,2	MCF-7	breast:

No data

Variant related genes	Relation type
GIMAP5	CpG island
ENSG00000213203	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11762727	0.83[GIH][hapmap];0.84[JPT][hapmap]
rs11983675	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12703097	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13240273	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13240287	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13247782	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17173582	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1860871	0.88[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2041574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075078	0.92[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs2109999	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2159842	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293172	0.83[GIH][hapmap]
rs2373802	0.84[JPT][hapmap]
rs2373850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34443555	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34531981	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35370936	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35662160	0.88[EUR][1000 genomes]
rs3735077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62490382	0.86[EUR][1000 genomes]
rs62490385	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67727004	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6945478	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6971135	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6978252	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7798682	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9690530	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9691508	0.83[GIH][hapmap];0.84[JPT][hapmap]

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
rs2286900	GIMAP5	cis	lymphoblastoid	seeQTL
rs2286900	TMEM176A	cis	cerebellum	SCAN
rs2286900	CNTNAP2	cis	cerebellum	SCAN
rs2286900	IAN4L1	cis	multi-tissue	Pritchard
rs2286900	TMEM176B	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150414000-150419400	Weak transcription	Fetal Lung	lung
2	chr7:150414400-150419200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr7:150414400-150419600	Weak transcription	Gastric	stomach
4	chr7:150414600-150421800	Weak transcription	Fetal Intestine Small	intestine
5	chr7:150415200-150419000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:150415200-150419200	Weak transcription	Brain Substantia Nigra	brain
7	chr7:150415200-150419400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr7:150415200-150420400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
9	chr7:150415200-150424800	Weak transcription	Pancreas	Pancrea
10	chr7:150415400-150419000	Weak transcription	Fetal Muscle Leg	muscle
11	chr7:150415400-150419000	Weak transcription	Small Intestine	intestine
12	chr7:150415400-150419200	Weak transcription	Brain Hippocampus Middle	brain
13	chr7:150415600-150419600	Weak transcription	Right Ventricle	heart
14	chr7:150415800-150418400	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr7:150415800-150418400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
16	chr7:150415800-150419400	Weak transcription	Liver	Liver
17	chr7:150415800-150420800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:150416000-150419200	Weak transcription	Brain Anterior Caudate	brain
19	chr7:150416000-150419400	Strong transcription	Fetal Thymus	thymus
20	chr7:150416000-150420200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:150416200-150418200	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
22	chr7:150416200-150419000	Strong transcription	HUVEC	blood vessel
23	chr7:150416200-150420600	Genic enhancers	Primary monocytes fromperipheralblood	blood
24	chr7:150416200-150420800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
25	chr7:150416400-150419400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:150416400-150419400	Weak transcription	Right Atrium	heart
27	chr7:150416400-150419600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr7:150416600-150418200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:150416600-150419000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr7:150416600-150419400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr7:150416800-150419000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr7:150416800-150422000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr7:150417000-150418200	Genic enhancers	Adipose Nuclei	Adipose
34	chr7:150417000-150419200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr7:150417200-150419400	Weak transcription	Fetal Brain Male	brain
36	chr7:150417400-150420000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
37	chr7:150417400-150423400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr7:150417600-150418200	Active TSS	Duodenum Mucosa	Duodenum
39	chr7:150417600-150419400	Weak transcription	Left Ventricle	heart
40	chr7:150417800-150419800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr7:150417800-150419800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr7:150417800-150419800	Weak transcription	Placenta	Placenta
43	chr7:150417800-150420000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr7:150417800-150422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr7:150417800-150423400	Weak transcription	Thymus	Thymus
46	chr7:150418000-150418800	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
47	chr7:150418000-150419000	Weak transcription	Lung	lung
48	chr7:150418000-150419000	Strong transcription	Dnd41	blood
49	chr7:150418000-150419200	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr7:150418000-150419200	Strong transcription	Spleen	Spleen

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