Variant report

Variant	rs4725905
Chromosome Location	chr7:150212634-150212635
allele	A/C
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	TAF1	chr7:150211806-150212653	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:150211830-150212674	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr7:150211694-150212708	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr7:150211611-150213235	GM12891	blood:	n/a	n/a
5	POLR2A	chr7:150211428-150213403	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
STRADBP1	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11762727	0.85[CEU][hapmap];1.00[LWK][hapmap]
rs11771561	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs12703077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12703083	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs13222905	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs13226709	0.98[EUR][1000 genomes]
rs13231883	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs13232597	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs13242186	0.92[CEU][hapmap];1.00[LWK][hapmap]
rs1568627	0.85[CEU][hapmap]
rs2177188	0.85[CEU][hapmap]
rs2177189	0.92[JPT][hapmap]
rs2293172	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs2293174	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs2373802	0.83[CEU][hapmap]
rs2373815	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs35104209	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3735079	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4725906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56330403	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62501523	1.00[EUR][1000 genomes]
rs9691508	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1031309	chr7:150171651-150222230	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4725905	GIMAP4	cis	lymphoblastoid	seeQTL
rs4725905	GIMAP5	cis	lymphoblastoid	seeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150211000-150213200	Active TSS	Lung	lung
2	chr7:150211000-150214600	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr7:150211000-150214800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
4	chr7:150211000-150216200	Active TSS	Psoas Muscle	Psoas
5	chr7:150211000-150219000	Active TSS	Right Atrium	heart
6	chr7:150211200-150213000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:150211200-150214800	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr7:150211200-150217000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr7:150211400-150214600	Active TSS	Brain Anterior Caudate	brain
10	chr7:150211400-150215400	Active TSS	Left Ventricle	heart
11	chr7:150211400-150217400	Active TSS	Adipose Nuclei	Adipose
12	chr7:150211400-150218600	Active TSS	Duodenum Mucosa	Duodenum
13	chr7:150211600-150213000	Active TSS	Brain Hippocampus Middle	brain
14	chr7:150211600-150213000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr7:150211600-150213200	Active TSS	Brain Cingulate Gyrus	brain
16	chr7:150211600-150213200	Active TSS	Brain Substantia Nigra	brain
17	chr7:150211600-150213200	Active TSS	Esophagus	oesophagus
18	chr7:150211600-150213400	Active TSS	Fetal Intestine Small	intestine
19	chr7:150211600-150214200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:150211600-150214200	Active TSS	Fetal Intestine Large	intestine
21	chr7:150211600-150214600	Active TSS	Stomach Smooth Muscle	stomach
22	chr7:150211600-150214800	Active TSS	Liver	Liver
23	chr7:150211600-150215400	Active TSS	Rectal Smooth Muscle	rectum
24	chr7:150211600-150215400	Active TSS	Right Ventricle	heart
25	chr7:150211600-150215400	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr7:150211600-150215800	Active TSS	Monocytes-CD14+_RO01746	blood
27	chr7:150211600-150216000	Active TSS	Fetal Muscle Leg	muscle
28	chr7:150211600-150216800	Active TSS	Primary monocytes fromperipheralblood	blood
29	chr7:150211600-150216800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr7:150211600-150217000	Active TSS	Primary T cells from cord blood	blood
31	chr7:150211600-150217000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr7:150211800-150213200	Active TSS	Fetal Muscle Trunk	muscle
33	chr7:150211800-150213600	Active TSS	Fetal Stomach	stomach
34	chr7:150211800-150214200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr7:150211800-150214800	Active TSS	Fetal Kidney	kidney
36	chr7:150211800-150215400	Active TSS	Thymus	Thymus
37	chr7:150211800-150216200	Active TSS	GM12878-XiMat	blood
38	chr7:150211800-150216800	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr7:150211800-150216800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr7:150211800-150216800	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr7:150211800-150217000	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr7:150212000-150212800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
43	chr7:150212000-150213000	Active TSS	Colon Smooth Muscle	Colon
44	chr7:150212000-150213200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
45	chr7:150212000-150213200	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr7:150212000-150213200	Active TSS	Gastric	stomach
47	chr7:150212000-150213200	Active TSS	Pancreas	Pancrea
48	chr7:150212000-150213200	Active TSS	Spleen	Spleen
49	chr7:150212000-150213400	Active TSS	Dnd41	blood
50	chr7:150212000-150214000	Active TSS	Placenta	Placenta

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