Variant report

Variant	rs1325267
Chromosome Location	chr1:67160814-67160815
allele	C/T
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	CTCF	chr1:67160801-67160841	GM10266	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCTEX1D1-3	chr1:67160734-67161176	NONHSAT003762

Variant related genes	Relation type
SGIP1	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11208941	0.87[AMR][1000 genomes]
rs1159851	0.84[MEX][hapmap]
rs12035546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12035592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12039010	0.87[AMR][1000 genomes]
rs12125455	0.84[MEX][hapmap]
rs12131909	0.84[MEX][hapmap]
rs12565436	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12726588	0.85[MEX][hapmap]
rs12728269	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12746750	0.85[AMR][1000 genomes]
rs1570814	0.89[MEX][hapmap]
rs17129322	0.89[YRI][hapmap]
rs17129332	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17129375	0.89[YRI][hapmap]
rs17129381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17129384	0.89[YRI][hapmap]
rs1853772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1975523	0.84[MEX][hapmap]
rs34093441	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34868698	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35393617	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4655625	0.84[MEX][hapmap]
rs67687377	0.87[AMR][1000 genomes]
rs9633417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1325267	KRTAP12-2	trans	cerebellum	SCAN
rs1325267	JAK1	cis	cerebellum	SCAN
rs1325267	WLS	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67140600-67161200	Weak transcription	Esophagus	oesophagus
2	chr1:67149200-67161000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:67152000-67162800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:67153400-67161200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:67155600-67167400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:67155800-67164600	Weak transcription	Fetal Brain Male	brain
7	chr1:67155800-67168200	Weak transcription	Fetal Heart	heart
8	chr1:67155800-67177200	Weak transcription	Brain Anterior Caudate	brain
9	chr1:67156000-67161400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:67156000-67177200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:67156200-67164400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:67156800-67166800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:67156800-67167600	Weak transcription	Brain Substantia Nigra	brain
14	chr1:67156800-67191400	Weak transcription	Fetal Brain Female	brain
15	chr1:67157000-67208800	Weak transcription	Brain Germinal Matrix	brain
16	chr1:67157200-67189600	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:67157400-67162200	Weak transcription	Fetal Intestine Large	intestine
18	chr1:67157400-67191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:67157600-67169400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:67158200-67189400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:67158400-67191400	Weak transcription	Left Ventricle	heart
22	chr1:67158600-67166600	Weak transcription	NH-A	brain
23	chr1:67158600-67189400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:67159600-67161400	Strong transcription	NHLF	lung
25	chr1:67159800-67161000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:67159800-67169600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:67160000-67169600	Weak transcription	NHDF-Ad	bronchial
28	chr1:67160200-67161200	Enhancers	Fetal Intestine Small	intestine
29	chr1:67160200-67169600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:67160400-67189400	Weak transcription	Brain Angular Gyrus	brain
31	chr1:67160600-67161200	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr1:67160600-67161200	Active TSS	Duodenum Mucosa	Duodenum
33	chr1:67160600-67161400	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:67160800-67161000	Enhancers	Lung	lung
35	chr1:67160800-67161200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:67160800-67161200	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr1:67160800-67161200	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr1:67160800-67161200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:67160800-67161200	Strong transcription	Aorta	Aorta

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