Variant report

Variant	rs57346147
Chromosome Location	chr3:47410564-47410565
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47406931..47409184-chr3:47410289..47412513,2	K562	blood:
2	chr3:47409105..47415396-chr3:47419096..47424075,13	K562	blood:
3	chr3:47327849..47330607-chr3:47409211..47411755,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000076201	Chromatin interaction
ENSG00000260236	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1038394	0.97[EUR][1000 genomes]
rs10865946	0.99[EUR][1000 genomes]
rs11130127	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130128	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130129	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130132	0.83[EUR][1000 genomes]
rs11130133	0.81[EUR][1000 genomes]
rs11705957	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11711265	0.81[EUR][1000 genomes]
rs11711824	0.96[EUR][1000 genomes]
rs11712445	0.99[EUR][1000 genomes]
rs11716763	0.86[EUR][1000 genomes]
rs11719877	0.99[EUR][1000 genomes]
rs11914913	0.81[EUR][1000 genomes]
rs11914932	0.81[EUR][1000 genomes]
rs11925823	0.99[EUR][1000 genomes]
rs11927371	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12486969	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12487736	0.90[EUR][1000 genomes]
rs12489046	0.86[EUR][1000 genomes]
rs12490058	0.83[EUR][1000 genomes]
rs12492433	0.86[EUR][1000 genomes]
rs12497225	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12630641	0.81[EUR][1000 genomes]
rs12632132	0.90[EUR][1000 genomes]
rs12636851	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13059519	0.82[EUR][1000 genomes]
rs13064843	0.99[EUR][1000 genomes]
rs13075233	0.99[EUR][1000 genomes]
rs13079098	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1531875	0.98[EUR][1000 genomes]
rs17411375	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17784882	0.83[EUR][1000 genomes]
rs1872164	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2062278	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2101247	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2159400	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291298	0.81[EUR][1000 genomes]
rs295428	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs295449	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs295458	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs295461	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3736177	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3816779	0.81[EUR][1000 genomes]
rs4241548	0.92[EUR][1000 genomes]
rs4858805	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4858848	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4858868	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4858888	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858890	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858894	0.86[EUR][1000 genomes]
rs553989	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56032309	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56351005	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59586735	0.86[EUR][1000 genomes]
rs60369822	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62246474	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62248580	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62248599	0.85[EUR][1000 genomes]
rs6765990	0.82[EUR][1000 genomes]
rs6780013	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6787422	0.99[EUR][1000 genomes]
rs6792461	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6792488	0.87[EUR][1000 genomes]
rs6800271	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73081205	0.84[EUR][1000 genomes]
rs7613282	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7628631	0.81[EUR][1000 genomes]
rs7641010	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7649234	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7651194	0.82[EUR][1000 genomes]
rs7651762	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs807810	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs807931	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8180040	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs878659	0.88[EUR][1000 genomes]
rs922957	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9683033	0.87[EUR][1000 genomes]
rs9683177	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv3802	chr3:47396674-47441951	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs57346147	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs57346147	SETD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47401600-47421200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:47404400-47411000	Weak transcription	Right Atrium	heart
3	chr3:47407400-47412600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:47407600-47412200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr3:47407600-47412600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:47407800-47412000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr3:47409800-47412400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:47410000-47410800	Enhancers	HepG2	liver
9	chr3:47410000-47411200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr3:47410200-47412400	Weak transcription	Primary B cells from cord blood	blood
11	chr3:47410400-47410600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:47410400-47410800	Enhancers	K562	blood

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