Variant report

Variant	rs2175409
Chromosome Location	chr4:152701656-152701657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152695897..152698227-chr4:152700601..152702140,2	K562	blood:
2	chr4:152689260..152690955-chr4:152700290..152702808,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10001603	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10013612	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10016160	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10222838	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10222925	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11099828	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11099829	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11723227	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12331037	0.85[GIH][hapmap]
rs12502446	0.91[ASN][1000 genomes]
rs12503677	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12506000	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12641433	0.96[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12641438	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12641441	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12647420	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12647462	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12647465	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12647616	0.86[EUR][1000 genomes]
rs13108359	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13119490	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13121178	0.80[EUR][1000 genomes]
rs13121190	0.84[EUR][1000 genomes]
rs13139327	0.85[EUR][1000 genomes]
rs13145446	0.80[EUR][1000 genomes]
rs13147021	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1366907	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1397683	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1429558	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1429559	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17360475	0.85[GIH][hapmap]
rs1877185	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1877186	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1877188	0.88[CEU][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2007218	0.82[GIH][hapmap]
rs2089811	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303866	0.94[JPT][hapmap]
rs2406973	0.96[CEU][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2406974	0.82[EUR][1000 genomes]
rs28659854	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3749561	0.80[GIH][hapmap]
rs3792691	0.82[GIH][hapmap]
rs3805356	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811794	0.83[AFR][1000 genomes]
rs3828546	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4399967	0.85[EUR][1000 genomes]
rs4554052	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4643789	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4696106	0.84[EUR][1000 genomes]
rs4696107	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4696108	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4696109	0.85[GIH][hapmap]
rs4696110	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696286	0.84[EUR][1000 genomes]
rs4696287	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4696290	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696293	0.85[GIH][hapmap]
rs4696295	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696296	0.81[ASN][1000 genomes]
rs4696297	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58751443	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59350867	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61308159	0.85[EUR][1000 genomes]
rs6535816	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6535818	0.85[GIH][hapmap]
rs6535819	0.85[GIH][hapmap]
rs6535822	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6816002	0.82[EUR][1000 genomes]
rs6847844	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6849111	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6855883	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6857073	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7654294	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7669465	0.96[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7669761	0.96[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7669977	0.85[GIH][hapmap]
rs7675818	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs867800	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9996320	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv4552	chr4:152681211-152702457	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2175409	PET112L	cis	cerebellum	SCAN
rs2175409	PET112L	cis	multi-tissue	Pritchard
rs2175409	PET112L	cis	Lymphoblastoid	GTEx
rs2175409	FAM160A1	cis	cerebellum	SCAN
rs2175409	PET112L	cis	parietal	SCAN
rs2175409	PET112L	cis	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152700800-152702600	Enhancers	Fetal Brain Male	brain
2	chr4:152701200-152703600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:152701400-152701800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:152701400-152701800	Enhancers	Left Ventricle	heart
5	chr4:152701400-152702600	Enhancers	Fetal Heart	heart
6	chr4:152701600-152703200	Enhancers	Brain Germinal Matrix	brain

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