Variant report

Variant	rs13005184
Chromosome Location	chr2:101196111-101196112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1052117	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1114285	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12616005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs1401753	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1533655	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1589246	1.00[JPT][hapmap]
rs17024338	1.00[JPT][hapmap]
rs2139402	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2309846	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2946587	0.81[AMR][1000 genomes]
rs2970994	0.84[AMR][1000 genomes]
rs2970997	1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs2971007	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4851332	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4851333	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6542968	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6542969	1.00[JPT][hapmap]
rs6747613	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6753993	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7575538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs7578708	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs7594904	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7595492	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv582532	chr2:101029002-101531943	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv834312	chr2:101044438-101238166	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13005184	STARD7	cis	cerebellum	SCAN
rs13005184	LONRF2	cis	parietal	SCAN
rs13005184	LMAN2L	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101180600-101197800	Weak transcription	Stomach Mucosa	stomach
2	chr2:101180800-101196800	Weak transcription	NHLF	lung
3	chr2:101180800-101197000	Weak transcription	Colonic Mucosa	Colon
4	chr2:101180800-101197200	Weak transcription	Small Intestine	intestine
5	chr2:101181400-101196200	Weak transcription	Gastric	stomach
6	chr2:101181400-101196800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:101181600-101196600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:101181600-101197200	Weak transcription	Brain Angular Gyrus	brain
9	chr2:101183800-101204200	Weak transcription	Hela-S3	cervix
10	chr2:101184000-101197600	Weak transcription	NHEK	skin
11	chr2:101184200-101196400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:101184200-101197600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:101186400-101197000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:101187600-101196600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr2:101188400-101196400	Weak transcription	Psoas Muscle	Psoas
16	chr2:101188400-101197200	Weak transcription	Spleen	Spleen
17	chr2:101188600-101196600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:101188600-101196600	Weak transcription	Thymus	Thymus
19	chr2:101188600-101197000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:101188600-101197400	Weak transcription	HSMMtube	muscle
21	chr2:101188600-101204200	Weak transcription	K562	blood
22	chr2:101188800-101197000	Weak transcription	Brain Anterior Caudate	brain
23	chr2:101188800-101197200	Weak transcription	Osteobl	bone
24	chr2:101189200-101196800	Weak transcription	Brain Germinal Matrix	brain
25	chr2:101189800-101196600	Weak transcription	Fetal Thymus	thymus
26	chr2:101190400-101196400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:101191200-101197600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:101191400-101197000	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:101191600-101196400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:101191600-101196600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:101191600-101197800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:101192000-101197200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:101192400-101197000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:101192400-101197200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:101192600-101197000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:101192600-101197000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:101192800-101196200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:101192800-101197000	Weak transcription	Brain Substantia Nigra	brain
39	chr2:101192800-101197000	Weak transcription	Fetal Brain Female	brain
40	chr2:101193000-101196600	Weak transcription	Primary B cells from cord blood	blood
41	chr2:101193000-101197000	Weak transcription	HUVEC	blood vessel
42	chr2:101193000-101197200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:101193000-101197200	Weak transcription	HepG2	liver
44	chr2:101193000-101197400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:101193200-101197000	Weak transcription	Esophagus	oesophagus
46	chr2:101193200-101197600	Weak transcription	Fetal Intestine Small	intestine
47	chr2:101193400-101197200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:101193600-101197400	Weak transcription	NH-A	brain
49	chr2:101194000-101196600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:101194200-101197200	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links