Variant report

Variant	rs17389112
Chromosome Location	chr1:85925235-85925236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1241320	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13373844	0.91[ASW][hapmap];0.90[CEU][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs1523993	0.91[GIH][hapmap]
rs17388780	0.87[ASN][1000 genomes]
rs36104818	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs527762	0.87[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs529582	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs582145	0.83[GIH][hapmap]
rs597168	0.87[CEU][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61223539	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61783057	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673833	0.81[ASW][hapmap];0.81[CEU][hapmap];0.91[GIH][hapmap]
rs7555486	0.90[CEU][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17389112	SYDE2	cis	cerebellum	SCAN
rs17389112	LOC339524	cis	cerebellum	SCAN
rs17389112	BCL10	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85915200-85927800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:85915600-85925400	Weak transcription	Brain Germinal Matrix	brain
3	chr1:85917400-85926400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:85917400-85929400	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:85917400-85929400	Weak transcription	Gastric	stomach
6	chr1:85917400-85929800	Weak transcription	Esophagus	oesophagus
7	chr1:85917800-85927200	Weak transcription	NH-A	brain
8	chr1:85917800-85928800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:85919200-85928400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:85919400-85927200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:85919600-85928200	Weak transcription	Fetal Brain Female	brain
12	chr1:85920000-85929600	Weak transcription	Brain Substantia Nigra	brain
13	chr1:85920200-85925400	Weak transcription	Ovary	ovary
14	chr1:85920200-85926400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:85920200-85928000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:85920400-85926400	Weak transcription	NHLF	lung
17	chr1:85920800-85929000	Weak transcription	HSMMtube	muscle
18	chr1:85922200-85925400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:85922600-85928400	Enhancers	Fetal Intestine Large	intestine
20	chr1:85922600-85929000	Enhancers	Fetal Intestine Small	intestine
21	chr1:85923200-85925800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:85923200-85926200	Enhancers	Stomach Mucosa	stomach
23	chr1:85923200-85927000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:85923200-85929800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:85923400-85925400	Enhancers	Fetal Stomach	stomach
26	chr1:85923600-85927000	Enhancers	HepG2	liver
27	chr1:85923600-85928200	Enhancers	Liver	Liver
28	chr1:85923800-85925800	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr1:85923800-85926200	Enhancers	Rectal Smooth Muscle	rectum
30	chr1:85924000-85925800	Weak transcription	HSMM	muscle
31	chr1:85924000-85925800	Weak transcription	Osteobl	bone
32	chr1:85924000-85926000	Enhancers	Fetal Lung	lung
33	chr1:85924200-85925400	Enhancers	Small Intestine	intestine
34	chr1:85924200-85926800	Enhancers	Colon Smooth Muscle	Colon
35	chr1:85924400-85927800	Weak transcription	Pancreas	Pancrea
36	chr1:85924600-85927800	Enhancers	HUVEC	blood vessel
37	chr1:85924800-85925800	Enhancers	Fetal Kidney	kidney
38	chr1:85924800-85926000	Enhancers	Duodenum Mucosa	Duodenum
39	chr1:85924800-85927200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:85924800-85928400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:85925000-85925400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:85925000-85925400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr1:85925000-85925400	Enhancers	Adipose Nuclei	Adipose
44	chr1:85925000-85925400	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr1:85925000-85925400	Flanking Active TSS	NHDF-Ad	bronchial
46	chr1:85925000-85925600	Enhancers	Fetal Brain Male	brain
47	chr1:85925000-85925600	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr1:85925000-85927000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:85925000-85928600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:85925000-85928800	Enhancers	Cortex derived primary cultured neurospheres	brain

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