Variant report

Variant	rs13020260
Chromosome Location	chr2:187612651-187612652
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187610996..187613793-chr2:187616587..187618211,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10165992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1072901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12471718	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12475476	1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs12618322	0.88[CHB][hapmap]
rs12620821	0.88[CHB][hapmap]
rs1448427	0.88[CHB][hapmap]
rs17406346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2012128	0.88[ASN][1000 genomes]
rs2012401	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2121975	0.88[CHB][hapmap]
rs2121976	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2276562	0.91[ASN][1000 genomes]
rs2290083	0.89[ASN][1000 genomes]
rs2595383	0.86[ASN][1000 genomes]
rs2595384	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2595386	0.87[ASN][1000 genomes]
rs2595395	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[ASN][1000 genomes]
rs2682863	0.95[ASN][1000 genomes]
rs2682868	0.89[ASN][1000 genomes]
rs2682873	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs3114941	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3213964	0.88[CHB][hapmap]
rs35540241	0.81[ASN][1000 genomes]
rs3768781	0.84[CHB][hapmap]
rs3768785	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs3816375	0.88[CHB][hapmap]
rs3911238	0.84[CHB][hapmap]
rs41265951	0.87[ASN][1000 genomes]
rs4666713	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4667108	0.88[CHB][hapmap]
rs4667112	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4667113	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55781198	0.81[ASN][1000 genomes]
rs62173041	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62173045	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62196185	0.92[ASN][1000 genomes]
rs6705757	0.88[CHB][hapmap]
rs718259	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7585442	0.88[CHB][hapmap]
rs7585471	0.88[CHB][hapmap]
rs930657	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs9967663	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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	nsv428069	chr2:187575692-187766209	ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13020260	STRA6	trans	cerebellum	SCAN
rs13020260	TFPI	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187592200-187618600	Weak transcription	Osteobl	bone
2	chr2:187596600-187626200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:187598600-187621200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:187599600-187631000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:187600000-187613200	Weak transcription	Pancreas	Pancrea
6	chr2:187603000-187612800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:187603200-187626400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:187603200-187626600	Weak transcription	Fetal Stomach	stomach
9	chr2:187603400-187612800	Weak transcription	Brain Anterior Caudate	brain
10	chr2:187603400-187613000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:187603400-187626400	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:187603600-187626600	Weak transcription	Left Ventricle	heart
13	chr2:187603800-187612800	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:187603800-187621200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:187604000-187613200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:187604000-187618600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:187604800-187613000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:187605000-187626200	Weak transcription	NHDF-Ad	bronchial
19	chr2:187605000-187626400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:187605400-187612800	Weak transcription	Fetal Brain Female	brain
21	chr2:187605600-187619200	Weak transcription	Ovary	ovary
22	chr2:187606000-187612800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:187607000-187619600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:187607400-187626200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:187608600-187614800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:187608600-187616600	Weak transcription	Fetal Brain Male	brain
27	chr2:187608800-187621200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:187609600-187617400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:187609800-187616400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:187609800-187621400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:187610000-187619600	Weak transcription	NH-A	brain
32	chr2:187610000-187621200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:187610200-187612800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:187610200-187612800	Weak transcription	HUVEC	blood vessel
35	chr2:187610200-187616200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:187610800-187621200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:187611000-187621400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:187611000-187626400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:187611000-187628800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:187611000-187628800	Weak transcription	HSMM	muscle
41	chr2:187611400-187613000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:187611400-187616600	Weak transcription	Brain Angular Gyrus	brain
43	chr2:187611600-187613400	Weak transcription	Adipose Nuclei	Adipose
44	chr2:187611800-187613200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:187611800-187613400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:187611800-187615800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:187611800-187618600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr2:187611800-187623800	Weak transcription	Psoas Muscle	Psoas
49	chr2:187612000-187636200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:187612400-187614800	Strong transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links