Variant report

Variant	rs1317559
Chromosome Location	chr7:150267737-150267738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1568628	0.82[CEU][hapmap]
rs2272092	0.82[CEU][hapmap];0.87[CHB][hapmap];0.85[AFR][1000 genomes]
rs2888665	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4725919	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59385901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6464080	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs6946579	0.82[CEU][hapmap]
rs7794415	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
7	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
8	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
9	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
10	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1317559	GIMAP8	Cis_1M	lymphoblastoid	RTeQTL
rs1317559	GIMAP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150263800-150267800	Active TSS	Rectal Smooth Muscle	rectum
2	chr7:150264000-150268200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr7:150264400-150268200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr7:150264600-150267800	Active TSS	Primary B cells from cord blood	blood
5	chr7:150265200-150271400	Weak transcription	Gastric	stomach
6	chr7:150265400-150269000	Weak transcription	Fetal Intestine Small	intestine
7	chr7:150265600-150268200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:150266000-150268200	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
9	chr7:150266000-150268200	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:150266000-150268200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
11	chr7:150266200-150268600	Weak transcription	Fetal Intestine Large	intestine
12	chr7:150266200-150270600	Weak transcription	Thymus	Thymus
13	chr7:150266400-150268000	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
14	chr7:150266400-150268400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
15	chr7:150266600-150267800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr7:150266600-150268000	Weak transcription	Fetal Muscle Leg	muscle
17	chr7:150266600-150269000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr7:150266600-150269200	Weak transcription	Esophagus	oesophagus
19	chr7:150266600-150269200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr7:150266600-150269800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr7:150266800-150267800	Weak transcription	Brain Anterior Caudate	brain
22	chr7:150266800-150268200	Enhancers	Primary hematopoietic stem cells	blood
23	chr7:150266800-150268200	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
24	chr7:150266800-150268400	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
25	chr7:150266800-150268600	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
26	chr7:150267000-150268000	Transcr. at gene 5' and 3'	Left Ventricle	heart
27	chr7:150267000-150268200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr7:150267000-150268400	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
29	chr7:150267000-150269600	Genic enhancers	HUVEC	blood vessel
30	chr7:150267000-150270600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:150267000-150271400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr7:150267000-150272400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:150267200-150267800	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
34	chr7:150267200-150267800	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr7:150267200-150268000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
36	chr7:150267200-150268000	Enhancers	Brain Substantia Nigra	brain
37	chr7:150267200-150268200	Enhancers	Right Atrium	heart
38	chr7:150267200-150268400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
39	chr7:150267200-150268400	Genic enhancers	Placenta	Placenta
40	chr7:150267200-150268400	Genic enhancers	Spleen	Spleen
41	chr7:150267200-150268400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
42	chr7:150267200-150270000	ZNF genes & repeats	Lung	lung
43	chr7:150267200-150271400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
44	chr7:150267400-150268000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
45	chr7:150267400-150268200	ZNF genes & repeats	Liver	Liver
46	chr7:150267400-150268400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
47	chr7:150267400-150269000	Strong transcription	Fetal Thymus	thymus
48	chr7:150267400-150269400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr7:150267400-150269800	Weak transcription	Brain Hippocampus Middle	brain
50	chr7:150267600-150267800	Strong transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links