Variant report

Variant	rs12991272
Chromosome Location	chr2:178457339-178457340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10170667	0.87[CEU][hapmap];0.88[JPT][hapmap]
rs10196345	0.91[ASN][1000 genomes]
rs10201153	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1047884	0.83[CEU][hapmap]
rs10497500	0.85[JPT][hapmap]
rs10497501	0.94[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10497502	0.90[JPT][hapmap]
rs10497503	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs10497508	0.90[JPT][hapmap]
rs10930798	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10930799	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10930800	0.88[EUR][1000 genomes]
rs10930801	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11684320	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11689550	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12463893	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12469386	0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap]
rs12471741	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12612857	0.94[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs12615367	1.00[JPT][hapmap]
rs12616093	1.00[JPT][hapmap]
rs12618139	0.85[JPT][hapmap]
rs12622298	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13000048	0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs13004955	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs13013752	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13020788	0.84[CEU][hapmap]
rs13027299	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13403787	0.94[ASN][1000 genomes]
rs13404970	0.90[ASN][1000 genomes]
rs13417231	0.92[ASN][1000 genomes]
rs13420302	0.81[ASN][1000 genomes]
rs13430517	0.90[ASN][1000 genomes]
rs13432183	0.81[ASN][1000 genomes]
rs1348848	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs1348849	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs1348850	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs1374437	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs1405713	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1453370	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs1545364	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1548067	0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16865203	0.90[JPT][hapmap]
rs16865291	0.90[JPT][hapmap]
rs16865328	1.00[JPT][hapmap]
rs16865331	1.00[JPT][hapmap]
rs1975543	0.83[EUR][1000 genomes]
rs2060929	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs2084233	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs2121430	0.84[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap]
rs2166554	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2166558	0.84[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2364854	0.94[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs3213945	1.00[JPT][hapmap]
rs3769995	0.90[JPT][hapmap]
rs3769996	0.90[JPT][hapmap]
rs3769997	0.90[JPT][hapmap]
rs3770002	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs3902850	0.84[CEU][hapmap]
rs3927978	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4243388	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs4243390	0.89[EUR][1000 genomes]
rs4528793	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4893822	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs4893823	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs4893825	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs4893950	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs4893957	0.84[CEU][hapmap]
rs4893959	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs4893961	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4893962	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs4893965	0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4893966	0.82[EUR][1000 genomes]
rs4893969	0.83[CEU][hapmap]
rs57562172	0.90[ASN][1000 genomes]
rs59666005	0.90[ASN][1000 genomes]
rs6710575	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs6734528	0.84[CEU][hapmap]
rs6736390	0.84[CEU][hapmap]
rs6742951	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs6761593	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7559521	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7587604	0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs7604673	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs7606235	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs8941	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs9288004	0.90[ASN][1000 genomes]
rs9288005	0.90[ASN][1000 genomes]
rs952746	0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762964	chr2:178416394-178481818	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3506731	chr2:178416851-178482200	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3506732	chr2:178416851-178482200	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv3520312	chr2:178417102-178482200	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv3520313	chr2:178417102-178482200	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12991272	TTC30B	cis	parietal	SCAN
rs12991272	DKFZp451M2119	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178445000-178457800	Weak transcription	Right Ventricle	heart
2	chr2:178451600-178458400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:178451600-178461400	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:178456800-178457800	Weak transcription	Fetal Stomach	stomach
5	chr2:178456800-178458800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:178457200-178457600	Flanking Active TSS	HepG2	liver

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