Variant report

Variant	rs2904515
Chromosome Location	chr12:66863923-66863924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10219502	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10219504	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10219746	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10748046	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10784542	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10784543	0.81[ASN][1000 genomes]
rs10878426	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10878427	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10878428	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10878429	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10878430	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10878431	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10878432	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878433	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11176194	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11176198	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11176208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176210	0.81[ASN][1000 genomes]
rs11176216	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322827	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366637	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12366955	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12371843	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12372784	0.81[ASN][1000 genomes]
rs12809616	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12817312	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821519	1.00[JPT][hapmap]
rs12830991	0.81[ASN][1000 genomes]
rs1826545	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36196058	0.81[ASN][1000 genomes]
rs3891950	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4128160	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7309214	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961823	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs866954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883229	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs883230	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs883231	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs931512	0.81[ASN][1000 genomes]
rs952562	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs952563	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1051713	chr12:66745716-66889411	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1040682	chr12:66750103-67328053	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv832447	chr12:66785814-66990029	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv469459	chr12:66854354-66950289	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv559206	chr12:66854354-66950289	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2904515	PPM1H	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66849400-66866400	Weak transcription	Pancreas	Pancrea
2	chr12:66853000-66876200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:66856800-66868400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:66860200-66868400	Weak transcription	Esophagus	oesophagus

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