Variant report

Variant	rs12463708
Chromosome Location	chr2:149073944-149073945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10206881	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10469577	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677584	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11683055	0.86[EUR][1000 genomes]
rs12466076	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12473137	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12474154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13386157	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13388448	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13390004	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410839	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13411082	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13427917	0.87[EUR][1000 genomes]
rs16828491	0.84[GIH][hapmap]
rs16828558	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16828564	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17355354	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28773905	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4563168	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56178042	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61304079	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6430309	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724259	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724587	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577649	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7590235	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7590487	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2753542	chr2:149004714-149268503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1012275	chr2:149031668-149316793	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv523090	chr2:149037012-149110873	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12463708	RPAP2	trans	brain	seeQTL
rs12463708	ARID4B	trans	brain	seeQTL
rs12463708	PLCL2	trans	multi-tissue	Pritchard
rs12463708	HEPH	trans	multi-tissue	Pritchard
rs12463708	PEA15	trans	multi-tissue	Pritchard
rs12463708	KCNA1	trans	brain	seeQTL
rs12463708	CACNB4	trans	brain	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:149012800-149096000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:149031400-149079000	Weak transcription	Left Ventricle	heart
3	chr2:149056000-149076400	Weak transcription	Esophagus	oesophagus
4	chr2:149058600-149076400	Weak transcription	Aorta	Aorta
5	chr2:149059400-149100400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:149061200-149095800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:149063400-149080600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:149067200-149095800	Weak transcription	HSMM	muscle
9	chr2:149069000-149075600	Weak transcription	Fetal Intestine Large	intestine
10	chr2:149069200-149096400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:149069400-149077800	Weak transcription	Gastric	stomach
12	chr2:149069400-149096000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:149069400-149100200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:149069600-149075600	Weak transcription	Spleen	Spleen
15	chr2:149069800-149076400	Weak transcription	Right Ventricle	heart
16	chr2:149070400-149075600	Weak transcription	Fetal Lung	lung
17	chr2:149071000-149078000	Weak transcription	Pancreas	Pancrea
18	chr2:149071000-149105000	Weak transcription	Thymus	Thymus
19	chr2:149071200-149074400	Weak transcription	Brain Germinal Matrix	brain
20	chr2:149071200-149075000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:149071200-149077200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:149071400-149074800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:149071400-149100400	Weak transcription	Ovary	ovary
24	chr2:149071600-149075400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:149071600-149078600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:149071600-149094000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:149071800-149095800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:149071800-149100400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:149072800-149075600	Strong transcription	Primary T cells from cord blood	blood
30	chr2:149073800-149076200	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links