Variant report

Variant	rs2733269
Chromosome Location	chr12:41866717-41866718
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1026462	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1026464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10506191	0.81[JPT][hapmap]
rs10506192	0.81[JPT][hapmap]
rs10735993	0.85[ASN][1000 genomes]
rs10785235	0.90[JPT][hapmap]
rs10785258	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs10785261	0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs10785265	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10880063	0.81[JPT][hapmap]
rs10880067	0.81[JPT][hapmap]
rs11180834	0.80[JPT][hapmap]
rs11180851	0.81[JPT][hapmap]
rs11180863	0.81[JPT][hapmap]
rs11180864	0.81[JPT][hapmap]
rs1160748	0.83[MEX][hapmap]
rs1160749	0.84[MEX][hapmap]
rs11835941	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12817575	0.81[JPT][hapmap]
rs1350430	0.84[MEX][hapmap]
rs1379758	0.81[AMR][1000 genomes]
rs1379759	0.81[AMR][1000 genomes]
rs1379760	0.81[AMR][1000 genomes]
rs1379761	0.81[AMR][1000 genomes]
rs1379763	0.81[AMR][1000 genomes]
rs1379764	0.81[AMR][1000 genomes]
rs1379768	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1379769	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1379771	0.81[AMR][1000 genomes]
rs1379772	0.81[AMR][1000 genomes]
rs1379774	0.81[AMR][1000 genomes]
rs1405552	0.81[JPT][hapmap]
rs1458156	0.92[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.96[ASN][1000 genomes]
rs1458157	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1458158	0.92[ASW][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap]
rs1458160	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1458165	0.87[MEX][hapmap]
rs1471161	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs1527090	0.81[JPT][hapmap]
rs1870285	0.81[AMR][1000 genomes]
rs1870286	0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs1902906	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1902911	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs2034923	0.95[ASN][1000 genomes]
rs2125286	0.81[AMR][1000 genomes]
rs2125287	0.81[AMR][1000 genomes]
rs2199028	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2250003	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2250009	0.92[LWK][hapmap];0.84[MEX][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2253528	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2253633	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2253634	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2255035	0.81[AMR][1000 genomes]
rs2255145	0.81[AMR][1000 genomes]
rs2255152	0.81[AMR][1000 genomes]
rs2264905	0.92[ASN][1000 genomes]
rs2405920	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2405921	0.81[AMR][1000 genomes]
rs2468314	0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2468315	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2468316	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2468317	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2608689	0.81[AMR][1000 genomes]
rs2608690	0.81[AMR][1000 genomes]
rs2608692	0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs2608696	0.81[AMR][1000 genomes]
rs2608697	0.81[AMR][1000 genomes]
rs2608702	0.93[ASN][1000 genomes]
rs2608705	0.81[AMR][1000 genomes]
rs2608706	0.81[AMR][1000 genomes]
rs2608708	0.84[AFR][1000 genomes]
rs2608711	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2608714	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2608715	0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2608716	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2608718	0.81[AMR][1000 genomes]
rs2730802	0.81[AMR][1000 genomes]
rs2730803	0.92[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.96[ASN][1000 genomes]
rs2730807	0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2730814	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2730819	0.83[MEX][hapmap]
rs2730824	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2730827	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2730828	0.84[MEX][hapmap]
rs2730829	0.84[MEX][hapmap]
rs2730830	0.85[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];0.94[ASN][1000 genomes]
rs2733275	0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2733276	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2733278	0.83[AMR][1000 genomes]
rs2733280	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2733285	0.87[ASN][1000 genomes]
rs2733287	0.96[ASN][1000 genomes]
rs2733289	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2733290	0.94[ASN][1000 genomes]
rs2733292	0.94[ASN][1000 genomes]
rs2733293	0.84[MEX][hapmap]
rs2733298	0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs2733299	0.81[AMR][1000 genomes]
rs285556	0.84[MEX][hapmap]
rs285575	0.83[MEX][hapmap]
rs2897268	0.81[JPT][hapmap]
rs4584644	0.84[MEX][hapmap]
rs4768354	0.94[ASN][1000 genomes]
rs7298808	0.84[MEX][hapmap]
rs7960955	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs7963312	0.81[JPT][hapmap]
rs7966732	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs897973	0.84[MEX][hapmap]
rs930905	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs961337	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs981014	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs996356	0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2733269	PDZRN4	cis	brain	seeQTL
rs2733269	PDZRN4	cis	parietal	SCAN
rs2733269	PDZRN4	trans	brain	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41860200-41869200	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:41861400-41870000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr12:41861400-41870400	Weak transcription	Brain Anterior Caudate	brain
4	chr12:41862000-41869800	Weak transcription	Brain Germinal Matrix	brain
5	chr12:41862000-41870200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:41862200-41869400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:41866400-41867400	Active TSS	Fetal Intestine Large	intestine
8	chr12:41866400-41867400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr12:41866400-41867800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr12:41866600-41866800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:41866600-41867000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr12:41866600-41867200	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr12:41866600-41867400	Enhancers	HUES48 Cell Line	embryonic stem cell

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