Variant report

Variant	rs1453317
Chromosome Location	chr2:149090114-149090115
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10164630	0.88[ASN][1000 genomes]
rs10181225	0.91[ASN][1000 genomes]
rs10188234	0.91[ASN][1000 genomes]
rs10196090	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10198939	0.84[ASN][1000 genomes]
rs10208839	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10928395	0.84[ASN][1000 genomes]
rs11675979	0.91[EUR][1000 genomes]
rs11678688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs11683219	0.92[EUR][1000 genomes]
rs12053104	0.91[EUR][1000 genomes]
rs12469720	0.82[EUR][1000 genomes]
rs12470061	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12478120	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12615490	0.84[ASN][1000 genomes]
rs12616001	0.84[ASN][1000 genomes]
rs12618358	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12992721	0.84[ASN][1000 genomes]
rs13427268	0.82[ASN][1000 genomes]
rs1404185	0.91[ASN][1000 genomes]
rs1404187	0.82[EUR][1000 genomes]
rs1453318	0.84[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs1580063	0.84[ASN][1000 genomes]
rs17276501	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1869341	0.91[EUR][1000 genomes]
rs1916960	0.90[ASN][1000 genomes]
rs2167880	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2602358	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2656317	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2656319	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2656320	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2656324	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2656325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28831467	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2938705	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35177340	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35630407	0.84[ASN][1000 genomes]
rs4972277	0.91[EUR][1000 genomes]
rs4972278	0.92[EUR][1000 genomes]
rs4972347	0.92[EUR][1000 genomes]
rs4972355	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4972358	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62183965	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6708633	0.90[ASN][1000 genomes]
rs6723914	0.84[ASN][1000 genomes]
rs6734448	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6745934	0.81[ASN][1000 genomes]
rs6748825	0.84[ASN][1000 genomes]
rs7425880	0.84[ASN][1000 genomes]
rs7567204	0.91[ASN][1000 genomes]
rs7592019	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7606618	0.91[ASN][1000 genomes]
rs7607930	0.84[ASN][1000 genomes]
rs869595	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs949679	0.95[EUR][1000 genomes]
rs991554	0.87[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1012123	chr2:149078500-149151358	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1453317	CACNB4	cis	parietal	SCAN

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	chr2:149059400-149100400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:149061200-149095800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:149067200-149095800	Weak transcription	HSMM	muscle
5	chr2:149069200-149096400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:149069400-149096000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:149069400-149100200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:149071000-149105000	Weak transcription	Thymus	Thymus
9	chr2:149071400-149100400	Weak transcription	Ovary	ovary
10	chr2:149071600-149094000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:149071800-149095800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:149071800-149100400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:149075600-149093600	Weak transcription	Primary T cells from cord blood	blood
14	chr2:149079800-149093600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:149079800-149094000	Weak transcription	Left Ventricle	heart
16	chr2:149085400-149100400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:149086400-149099600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:149086400-149099800	Weak transcription	GM12878-XiMat	blood
19	chr2:149086600-149093600	Weak transcription	Primary B cells from cord blood	blood
20	chr2:149086800-149094000	Weak transcription	Dnd41	blood
21	chr2:149086800-149098200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:149086800-149100400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr2:149088400-149100400	Weak transcription	Fetal Kidney	kidney
24	chr2:149088800-149096200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:149089000-149094000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:149089200-149119400	Weak transcription	Fetal Intestine Small	intestine
27	chr2:149089600-149100400	Weak transcription	Fetal Intestine Large	intestine
28	chr2:149089600-149105400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:149089800-149096000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:149090000-149104200	Weak transcription	Primary T cells fromperipheralblood	blood

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