Variant report

Variant	rs13087347
Chromosome Location	chr3:113785818-113785819
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11926807	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13061658	0.85[ASN][1000 genomes]
rs13064372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13064466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13069900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070378	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13071100	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13086657	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13094677	0.81[EUR][1000 genomes]
rs13096290	0.96[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs1386478	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs1487265	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2242316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2632241	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2632259	0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324553	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324555	1.00[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324556	0.89[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35745351	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6775521	0.82[LWK][hapmap]
rs6809991	0.82[LWK][hapmap]
rs7620955	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7631864	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7638536	0.82[LWK][hapmap]

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	nsv877352	chr3:113744010-113870078	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13087347	KTELC1	cis	parietal	SCAN
rs13087347	CD80	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113776200-113789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:113776200-113795000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:113776400-113792400	Weak transcription	Esophagus	oesophagus
4	chr3:113776400-113794800	Weak transcription	Aorta	Aorta
5	chr3:113776400-113806800	Weak transcription	Stomach Mucosa	stomach
6	chr3:113776600-113786600	Weak transcription	Placenta	Placenta
7	chr3:113776600-113789400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:113776600-113789400	Weak transcription	HSMMtube	muscle
9	chr3:113776600-113790200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:113776600-113795600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:113776800-113786800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:113776800-113786800	Weak transcription	Fetal Stomach	stomach
13	chr3:113776800-113787400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:113776800-113789400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:113776800-113789400	Weak transcription	Thymus	Thymus
16	chr3:113776800-113789600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:113776800-113789800	Weak transcription	Brain Substantia Nigra	brain
18	chr3:113776800-113790000	Weak transcription	Psoas Muscle	Psoas
19	chr3:113776800-113790600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:113776800-113792600	Weak transcription	Right Ventricle	heart
21	chr3:113776800-113795200	Weak transcription	Brain Angular Gyrus	brain
22	chr3:113776800-113798600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:113777000-113786200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:113777000-113786600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:113777000-113786600	Weak transcription	Fetal Heart	heart
26	chr3:113777000-113789400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:113777000-113789600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:113777000-113789600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:113777000-113789600	Weak transcription	Colonic Mucosa	Colon
30	chr3:113777000-113789600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:113777000-113790000	Weak transcription	Fetal Brain Male	brain
32	chr3:113777000-113790200	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:113777000-113790800	Weak transcription	K562	blood
34	chr3:113777000-113792800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:113777200-113786400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:113777200-113790400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:113777200-113790400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:113777200-113791400	Weak transcription	NHLF	lung
39	chr3:113777400-113789000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:113777400-113790600	Weak transcription	Brain Germinal Matrix	brain
41	chr3:113777600-113786800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:113777800-113790000	Weak transcription	Gastric	stomach
43	chr3:113777800-113794400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:113778000-113786600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:113778000-113786600	Weak transcription	NH-A	brain
46	chr3:113778200-113789600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:113779000-113786400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:113780000-113786600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:113780400-113789400	Weak transcription	Spleen	Spleen
50	chr3:113780400-113790400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links