Variant report

Variant	rs12518404
Chromosome Location	chr5:60341996-60341997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr5:60341940-60342255	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60334340..60336285-chr5:60341216..60344077,2	K562	blood:

Variant related genes	Relation type
NDUFAF2	TF binding region

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1021005	0.82[EUR][1000 genomes]
rs10805374	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10939879	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10939881	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11739952	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12516995	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12517310	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12518792	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12652830	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12652878	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12653132	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12655209	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12655603	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1382917	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1460961	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1471488	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1479645	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1526896	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs159535	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs159536	0.94[EUR][1000 genomes]
rs17332824	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17392014	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17419290	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17444495	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1983484	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2049579	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2120956	0.82[EUR][1000 genomes]
rs2120957	0.82[EUR][1000 genomes]
rs28436304	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2898309	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34608	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34619	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3797559	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4642318	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647052	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4647132	0.81[EUR][1000 genomes]
rs4647150	0.83[EUR][1000 genomes]
rs4700402	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4700404	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4700407	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55738840	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55814394	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56025209	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56031340	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56284222	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56350217	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58646987	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60858663	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61017995	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61101592	0.82[EUR][1000 genomes]
rs62365455	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62365458	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62367862	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62367872	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62367878	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62367879	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62367885	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62367903	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62372103	0.82[ASN][1000 genomes]
rs62372133	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62372134	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6449512	0.85[EUR][1000 genomes]
rs67490467	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67555188	0.82[ASN][1000 genomes]
rs67858932	0.82[ASN][1000 genomes]
rs68104763	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6884966	0.82[EUR][1000 genomes]
rs726824	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72757187	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72759206	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72759215	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7701398	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7709522	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7713481	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7714396	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7722373	0.90[ASN][1000 genomes]
rs7723349	0.92[ASN][1000 genomes]
rs7723901	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7734205	0.88[EUR][1000 genomes]
rs7737276	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs868791	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs888799	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9687099	0.82[EUR][1000 genomes]
rs976630	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs976631	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv881715	chr5:60116613-60356423	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv881717	chr5:60141245-60372582	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv869065	chr5:60180775-60428760	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv881721	chr5:60232646-60344399	Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv598313	chr5:60247815-60374912	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv881722	chr5:60266875-60384171	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1019307	chr5:60295350-60409077	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv3381326	chr5:60340145-60342093	Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12518404	ERCC8	Cis_1M	lymphoblastoid	RTeQTL
rs12518404	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60323000-60347000	Weak transcription	Primary B cells from cord blood	blood
2	chr5:60324600-60354000	Weak transcription	Primary T cells from cord blood	blood
3	chr5:60326000-60400800	Weak transcription	Left Ventricle	heart
4	chr5:60335600-60343800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr5:60339200-60343200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:60339800-60348200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr5:60340600-60343200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:60340600-60344200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:60340800-60342800	Weak transcription	Psoas Muscle	Psoas
10	chr5:60340800-60343600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links