Variant report

Variant	rs12582735
Chromosome Location	chr12:120034038-120034039
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr12:120033637-120034316	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr12:120033688-120034389	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr12:120033706-120034453	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr12:120033894-120034279	SK-N-SH	brain:	n/a	chr12:120034110-120034119
5	POLR2A	chr12:120033672-120034190	HUVEC	blood vessel:	n/a	n/a
6	FOS	chr12:120033520-120034083	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr12:120032501-120034200	U87	brain:	n/a	n/a
8	GATA3	chr12:120033675-120034404	SK-N-SH	brain:	n/a	n/a
9	GABPA	chr12:120033670-120034153	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr12:120033367-120034336	U87	brain:	n/a	n/a
11	PBX3	chr12:120033762-120034427	SK-N-SH	brain:	n/a	chr12:120034110-120034119
12	GABPA	chr12:120033675-120034166	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr12:120032336-120034342	U87	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000248636	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10744740	0.84[ASN][1000 genomes]
rs10744741	0.81[ASN][1000 genomes]
rs10744742	0.81[ASN][1000 genomes]
rs10774504	0.97[ASN][1000 genomes]
rs10774505	0.84[ASN][1000 genomes]
rs10849673	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs10849674	0.98[ASN][1000 genomes]
rs10849679	0.83[ASN][1000 genomes]
rs10849682	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10849683	0.81[ASN][1000 genomes]
rs11064843	0.82[ASN][1000 genomes]
rs11064855	0.81[ASN][1000 genomes]
rs1109856	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12422340	0.80[EUR][1000 genomes]
rs12425356	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12425649	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12425680	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12579854	0.96[ASN][1000 genomes]
rs12708371	0.81[ASN][1000 genomes]
rs12825063	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12825555	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12827937	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1303904	0.81[ASN][1000 genomes]
rs1476453	0.84[ASN][1000 genomes]
rs1544329	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16949411	0.80[EUR][1000 genomes]
rs2015795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2157806	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2893796	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3847956	0.84[ASN][1000 genomes]
rs4767829	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs4767830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4767831	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4767832	0.84[ASN][1000 genomes]
rs4767833	0.86[ASN][1000 genomes]
rs7295362	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7306273	0.84[ASN][1000 genomes]
rs7310741	0.82[ASN][1000 genomes]
rs739423	0.84[ASN][1000 genomes]
rs7954674	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7955433	0.94[ASN][1000 genomes]
rs7957284	0.82[ASN][1000 genomes]
rs7965791	0.81[ASN][1000 genomes]
rs7978341	0.82[ASN][1000 genomes]
rs7981024	0.82[ASN][1000 genomes]
rs9634163	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9634174	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][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	nsv916688	chr12:119801814-120044407	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv832529	chr12:119863378-120071646	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1052595	chr12:119992580-120132038	Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv541616	chr12:119992580-120132038	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12582735	TMEM233	cis	Thyroid	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120030800-120034800	Active TSS	HSMM	muscle
2	chr12:120031000-120034400	Active TSS	Psoas Muscle	Psoas
3	chr12:120031200-120034200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr12:120031400-120034200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr12:120031400-120034600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr12:120032200-120034200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:120032800-120034200	Active TSS	Osteobl	bone
8	chr12:120033200-120034200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr12:120033400-120034200	ZNF genes & repeats	Spleen	Spleen
10	chr12:120033400-120034200	Bivalent Enhancer	HepG2	liver
11	chr12:120033600-120034200	Flanking Active TSS	HSMMtube	muscle
12	chr12:120033600-120034800	Bivalent Enhancer	Adipose Nuclei	Adipose
13	chr12:120033600-120035000	Enhancers	HUVEC	blood vessel
14	chr12:120034000-120034200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
15	chr12:120034000-120034200	Flanking Active TSS	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links