Variant report

Variant	rs17553490
Chromosome Location	chr7:150263909-150263910
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	JUND	chr7:150263768-150264009	HepG2	liver:	n/a	chr7:150263862-150263873 chr7:150263864-150263872 chr7:150263862-150263874 chr7:150263864-150263871 chr7:150263863-150263873 chr7:150263863-150263872
2	FOS	chr7:150263803-150264462	HUVEC	blood vessel:	n/a	chr7:150263864-150263872 chr7:150263862-150263874 chr7:150263864-150263871 chr7:150263863-150263873 chr7:150263863-150263872

Variant related genes	Relation type
GIMAP4	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10215009	0.93[EUR][1000 genomes]
rs10216065	0.89[EUR][1000 genomes]
rs10226091	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10231133	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10231482	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10236504	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10240847	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10277380	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11982892	0.88[EUR][1000 genomes]
rs12537216	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12537905	0.85[EUR][1000 genomes]
rs1522596	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1522597	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1608157	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1916004	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1916011	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1916012	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2373810	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2373812	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28763707	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2888663	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34920034	0.89[EUR][1000 genomes]
rs4439037	0.93[EUR][1000 genomes]
rs4473934	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55855717	0.86[EUR][1000 genomes]
rs56194161	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62501527	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66873945	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6968637	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7778374	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7786392	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7788153	0.86[EUR][1000 genomes]
rs7788419	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7791295	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7796156	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7803206	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7803501	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9690525	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9691152	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
7	esv3395746	chr7:150181141-150300680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv3341786	chr7:150220353-150269134	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv16529	chr7:150249312-150312843	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	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
11	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17553490	GIMAP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150260400-150264600	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr7:150260800-150264200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:150260800-150265000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr7:150262000-150264400	Weak transcription	Fetal Stomach	stomach
5	chr7:150262000-150265000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr7:150262400-150264600	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr7:150262600-150264600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr7:150263000-150264400	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr7:150263000-150264400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr7:150263200-150264200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr7:150263200-150264200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr7:150263200-150264200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr7:150263400-150264200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr7:150263400-150264200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr7:150263400-150265200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr7:150263600-150264200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr7:150263600-150264200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr7:150263600-150264200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr7:150263600-150264200	Enhancers	HUVEC	blood vessel
20	chr7:150263600-150264400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr7:150263600-150264400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr7:150263800-150264200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr7:150263800-150264200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr7:150263800-150264200	Enhancers	Left Ventricle	heart
25	chr7:150263800-150264200	Enhancers	Spleen	Spleen
26	chr7:150263800-150264400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr7:150263800-150264400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr7:150263800-150264600	Enhancers	H9 Cell Line	embryonic stem cell
29	chr7:150263800-150265200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:150263800-150265400	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr7:150263800-150266600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:150263800-150266800	Active TSS	Adipose Nuclei	Adipose
33	chr7:150263800-150267600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr7:150263800-150267800	Active TSS	Rectal Smooth Muscle	rectum

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