Variant report

Variant	rs12187606
Chromosome Location	chr5:118195109-118195110
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10447237	0.82[AFR][1000 genomes]
rs10519564	1.00[JPT][hapmap]
rs11949851	0.84[ASN][1000 genomes]
rs12109156	1.00[JPT][hapmap]
rs12659444	0.94[GIH][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1567521	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17132673	0.85[AFR][1000 genomes]
rs17132677	1.00[JPT][hapmap]
rs17144708	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17144714	1.00[CHB][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs17144715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17144716	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17144806	1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17144824	1.00[JPT][hapmap]
rs17144836	1.00[JPT][hapmap]
rs1864109	0.83[AFR][1000 genomes]
rs2099092	0.83[AFR][1000 genomes]
rs2115301	0.82[ASW][hapmap];1.00[CHB][hapmap];0.97[LWK][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs2115302	0.83[AFR][1000 genomes]
rs2162888	0.83[AFR][1000 genomes]
rs2217310	1.00[JPT][hapmap]
rs2377127	1.00[JPT][hapmap]
rs370827	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3813297	0.82[ASW][hapmap];1.00[CHB][hapmap];0.97[LWK][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs3813298	1.00[CHB][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs447317	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4634381	1.00[JPT][hapmap]
rs4895183	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4895184	0.82[CHB][hapmap]
rs4895347	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4895353	1.00[CHB][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs4895354	1.00[CHB][hapmap];0.92[LWK][hapmap];0.86[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs55821851	0.85[AFR][1000 genomes]
rs6860946	1.00[JPT][hapmap]
rs6861907	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6871241	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6874109	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6874399	1.00[JPT][hapmap]
rs6880144	1.00[JPT][hapmap]
rs6881583	0.82[AFR][1000 genomes]
rs6881776	0.89[ASN][1000 genomes]
rs6886240	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6892437	1.00[JPT][hapmap]
rs73234489	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73234502	0.85[AFR][1000 genomes]
rs73236920	0.82[AFR][1000 genomes]
rs7709381	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7721907	1.00[JPT][hapmap]
rs7722027	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7726905	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7734815	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882767	chr5:117931730-118385691	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv599562	chr5:118122504-118230640	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv882771	chr5:118170135-118230640	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv882772	chr5:118173127-118230640	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv882773	chr5:118175640-118241854	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv599563	chr5:118191798-118241854	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12187606	TRIM36	cis	cerebellum	SCAN
rs12187606	HSD17B4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118169600-118208600	Weak transcription	Aorta	Aorta
2	chr5:118189400-118209400	Weak transcription	Primary T cells from cord blood	blood
3	chr5:118189600-118205400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:118189600-118210600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:118190600-118209000	Weak transcription	Left Ventricle	heart
6	chr5:118190800-118210000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:118193600-118205600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:118193800-118197000	Weak transcription	HMEC	breast
9	chr5:118193800-118197600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:118193800-118209200	Weak transcription	Pancreas	Pancrea
11	chr5:118194000-118197600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:118194000-118210200	Weak transcription	Primary B cells from cord blood	blood
13	chr5:118194200-118197600	Weak transcription	NHEK	skin
14	chr5:118194200-118198000	Weak transcription	Fetal Heart	heart
15	chr5:118194800-118208200	Weak transcription	Primary hematopoietic stem cells	blood

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