Variant report

Variant	rs12299762
Chromosome Location	chr12:41859112-41859113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10161143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10880077	0.92[EUR][1000 genomes]
rs12298084	0.92[EUR][1000 genomes]
rs12298553	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12300549	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12305318	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12305552	0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12307517	0.95[ASN][1000 genomes]
rs12313532	0.88[CEU][hapmap];1.00[EUR][1000 genomes]
rs12314242	0.97[ASN][1000 genomes]
rs12314473	0.92[EUR][1000 genomes]
rs12314805	0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs12322329	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes]
rs1350433	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1458155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1534277	0.93[JPT][hapmap]
rs17129267	0.93[JPT][hapmap]
rs17129287	0.93[JPT][hapmap]
rs17129295	0.93[JPT][hapmap]
rs17129296	0.93[JPT][hapmap]
rs17129305	0.93[JPT][hapmap]
rs17129347	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs17129351	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17129364	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17129405	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17129413	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17129441	0.91[CHB][hapmap]
rs1817270	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2254521	0.88[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.99[EUR][1000 genomes]
rs2405924	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2446145	0.93[EUR][1000 genomes]
rs2608698	0.93[EUR][1000 genomes]
rs2608699	0.93[EUR][1000 genomes]
rs2608713	0.94[GIH][hapmap];0.81[TSI][hapmap];0.93[EUR][1000 genomes]
rs2608717	0.85[MEX][hapmap]
rs2730812	0.83[GIH][hapmap]
rs2730815	0.93[EUR][1000 genomes]
rs2730825	0.93[EUR][1000 genomes]
rs2733288	0.94[GIH][hapmap];0.93[EUR][1000 genomes]
rs285559	0.83[GIH][hapmap]
rs285571	0.83[GIH][hapmap];0.85[MEX][hapmap]
rs285596	0.83[GIH][hapmap]
rs287087	0.83[GIH][hapmap]
rs2897270	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs35366617	0.92[EUR][1000 genomes]
rs3761676	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs56394503	0.86[ASN][1000 genomes]
rs58573939	0.95[ASN][1000 genomes]
rs59662716	0.95[ASN][1000 genomes]
rs60903037	0.99[ASN][1000 genomes]
rs7133340	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297699	0.97[ASN][1000 genomes]
rs7305541	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7307387	0.91[CHB][hapmap]
rs73274484	0.87[ASN][1000 genomes]
rs73278055	0.89[ASN][1000 genomes]
rs74077585	0.87[ASN][1000 genomes]
rs74077591	0.95[ASN][1000 genomes]
rs7960293	0.82[CHB][hapmap]
rs7966351	0.86[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	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	esv3501985	chr12:41847710-41863530	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
3	esv3501996	chr12:41847724-41863526	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
4	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12299762	PDZRN4	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41829600-41860600	Weak transcription	Aorta	Aorta
2	chr12:41848600-41860800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:41853400-41860200	Weak transcription	Brain Germinal Matrix	brain
4	chr12:41853800-41859200	Weak transcription	Fetal Lung	lung
5	chr12:41855000-41859400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:41855000-41860600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:41855000-41861000	Weak transcription	Brain Anterior Caudate	brain
8	chr12:41855200-41859400	Weak transcription	Brain Substantia Nigra	brain
9	chr12:41855400-41860600	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:41857600-41860200	Enhancers	Colon Smooth Muscle	Colon
11	chr12:41858000-41859400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:41858400-41863000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr12:41858800-41859200	Enhancers	Stomach Smooth Muscle	stomach
14	chr12:41858800-41859800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:41858800-41860200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:41859000-41862000	Enhancers	HUES48 Cell Line	embryonic stem cell

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