Variant report

Variant	rs55642497
Chromosome Location	chr7:150328567-150328568
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10231041	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10235151	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10243208	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253121	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10255380	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10258838	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10272462	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1071922	0.89[ASN][1000 genomes]
rs11763094	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11763374	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11768445	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11770532	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3088115	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3735084	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3735085	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57269277	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	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	esv3388935	chr7:150301204-150374532	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55642497	GIMAP6	Cis_1M	lymphoblastoid	RTeQTL
rs55642497	GIMAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150324000-150329200	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr7:150327400-150329400	Active TSS	Stomach Smooth Muscle	stomach
3	chr7:150327400-150329800	Active TSS	Duodenum Mucosa	Duodenum
4	chr7:150327600-150328600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr7:150327600-150329000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr7:150327600-150329200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
7	chr7:150327600-150329600	Active TSS	Placenta	Placenta
8	chr7:150327600-150329800	Active TSS	Esophagus	oesophagus
9	chr7:150327600-150329800	Active TSS	Rectal Smooth Muscle	rectum
10	chr7:150327600-150330000	Active TSS	Brain Hippocampus Middle	brain
11	chr7:150327600-150330000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr7:150327600-150330000	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr7:150327600-150330000	Flanking Active TSS	HUVEC	blood vessel
14	chr7:150327800-150328600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr7:150327800-150328800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr7:150327800-150328800	Flanking Active TSS	Fetal Thymus	thymus
17	chr7:150327800-150329400	Active TSS	Pancreas	Pancrea
18	chr7:150327800-150329600	Active TSS	Liver	Liver
19	chr7:150327800-150329600	Active TSS	Lung	lung
20	chr7:150327800-150329800	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr7:150327800-150330000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr7:150327800-150330000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:150327800-150330000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:150327800-150330000	Active TSS	Right Atrium	heart
25	chr7:150327800-150330200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:150328000-150328800	Flanking Active TSS	Thymus	Thymus
27	chr7:150328000-150329400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr7:150328000-150329400	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr7:150328000-150329600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr7:150328000-150329600	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr7:150328000-150329600	Active TSS	Adipose Nuclei	Adipose
32	chr7:150328000-150329600	Active TSS	Fetal Muscle Trunk	muscle
33	chr7:150328000-150329800	Active TSS	Brain Anterior Caudate	brain
34	chr7:150328000-150329800	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr7:150328000-150329800	Active TSS	Fetal Muscle Leg	muscle
36	chr7:150328000-150329800	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr7:150328000-150330000	Active TSS	Primary T cells fromperipheralblood	blood
38	chr7:150328000-150330000	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr7:150328000-150330000	Active TSS	Psoas Muscle	Psoas
40	chr7:150328200-150328600	Active TSS	Primary B cells from cord blood	blood
41	chr7:150328200-150329200	Active TSS	Spleen	Spleen
42	chr7:150328200-150329200	Enhancers	NHEK	skin
43	chr7:150328200-150329400	Active TSS	Brain Substantia Nigra	brain
44	chr7:150328200-150329400	Active TSS	Colonic Mucosa	Colon
45	chr7:150328200-150329400	Active TSS	Colon Smooth Muscle	Colon
46	chr7:150328200-150329400	Active TSS	Fetal Intestine Large	intestine
47	chr7:150328200-150329600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr7:150328200-150329600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr7:150328200-150329600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr7:150328200-150329600	Active TSS	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links