Variant report

Variant	rs62260741
Chromosome Location	chr3:47579965-47579966
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	chr3:47579787..47581854-chr3:47822138..47824570,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPN23-2	chr3:47578358-47580118	XLOC_002639

Variant related genes	Relation type
ENSG00000173473	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11130128	0.82[EUR][1000 genomes]
rs11130129	0.82[EUR][1000 genomes]
rs11130132	0.90[EUR][1000 genomes]
rs11130133	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130137	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11707895	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11711265	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11713413	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11716763	0.85[EUR][1000 genomes]
rs11914795	0.86[ASN][1000 genomes]
rs11914913	0.87[EUR][1000 genomes]
rs11914932	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12489046	0.84[EUR][1000 genomes]
rs12490058	0.89[EUR][1000 genomes]
rs12492433	0.84[EUR][1000 genomes]
rs12630641	0.90[EUR][1000 genomes]
rs13059519	0.91[EUR][1000 genomes]
rs1564760	0.92[ASN][1000 genomes]
rs1564761	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17784882	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1872166	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2101247	0.82[EUR][1000 genomes]
rs2291298	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34634681	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816779	0.90[EUR][1000 genomes]
rs4599332	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858856	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858894	0.80[EUR][1000 genomes]
rs59586735	0.85[EUR][1000 genomes]
rs62248599	0.83[EUR][1000 genomes]
rs62248605	0.85[EUR][1000 genomes]
rs62260710	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62260711	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6765990	0.91[EUR][1000 genomes]
rs6768879	0.89[ASN][1000 genomes]
rs6790763	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792488	0.81[EUR][1000 genomes]
rs73081205	0.83[EUR][1000 genomes]
rs7628631	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7649234	0.82[EUR][1000 genomes]
rs7651194	0.91[EUR][1000 genomes]
rs878659	0.82[EUR][1000 genomes]
rs9683033	0.82[EUR][1000 genomes]
rs9683177	0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62260741	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs62260741	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47577000-47583000	Weak transcription	K562	blood
2	chr3:47578600-47581000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:47578600-47582000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:47578600-47583800	Weak transcription	Brain Germinal Matrix	brain
5	chr3:47578800-47582600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:47578800-47586400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:47579200-47583000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:47579200-47583200	Weak transcription	Brain Anterior Caudate	brain
9	chr3:47579800-47582000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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