Variant report

Variant	rs34634681
Chromosome Location	chr3:47579102-47579103
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47577057..47579594-chr3:47584363..47586056,2	K562	blood:
2	chr3:47576235..47579154-chr3:47602909..47605701,2	K562	blood:
3	chr3:47576894..47579860-chr3:47580473..47582532,3	K562	blood:
4	chr3:47570695..47572679-chr3:47577270..47579482,2	K562	blood:

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

Variant related genes	Relation type
ENSG00000266443	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11130128	0.84[EUR][1000 genomes]
rs11130129	0.85[EUR][1000 genomes]
rs11130132	0.92[EUR][1000 genomes]
rs11130133	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130137	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707895	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711265	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11713413	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716763	0.87[EUR][1000 genomes]
rs11914795	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11914913	0.90[EUR][1000 genomes]
rs11914932	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489046	0.87[EUR][1000 genomes]
rs12490058	0.92[EUR][1000 genomes]
rs12492433	0.87[EUR][1000 genomes]
rs12630641	0.92[EUR][1000 genomes]
rs13059519	0.94[EUR][1000 genomes]
rs1564760	0.93[ASN][1000 genomes]
rs1564761	0.97[ASN][1000 genomes]
rs17784882	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1872166	0.97[ASN][1000 genomes]
rs2101247	0.85[EUR][1000 genomes]
rs2291298	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3816779	0.92[EUR][1000 genomes]
rs4599332	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858856	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858894	0.83[EUR][1000 genomes]
rs59586735	0.87[EUR][1000 genomes]
rs60369822	0.82[EUR][1000 genomes]
rs62248599	0.86[EUR][1000 genomes]
rs62248603	0.82[EUR][1000 genomes]
rs62248605	0.88[EUR][1000 genomes]
rs62260710	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62260711	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62260741	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6765990	0.94[EUR][1000 genomes]
rs6768879	0.90[ASN][1000 genomes]
rs6790763	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6792488	0.84[EUR][1000 genomes]
rs73081205	0.85[EUR][1000 genomes]
rs7628631	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7649234	0.84[EUR][1000 genomes]
rs7651194	0.94[EUR][1000 genomes]
rs878659	0.85[EUR][1000 genomes]
rs9683033	0.84[EUR][1000 genomes]
rs9683177	0.84[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
rs34634681	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs34634681	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47576800-47579800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr3:47577000-47583000	Weak transcription	K562	blood
3	chr3:47577600-47579200	Enhancers	Fetal Brain Male	brain
4	chr3:47578400-47579200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:47578400-47579200	Enhancers	Brain Anterior Caudate	brain
6	chr3:47578600-47579200	Bivalent Enhancer	HepG2	liver
7	chr3:47578600-47581000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:47578600-47582000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:47578600-47583800	Weak transcription	Brain Germinal Matrix	brain
10	chr3:47578800-47582600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:47578800-47586400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:47579000-47579200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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