Variant report

Variant	rs879242
Chromosome Location	chr12:48503301-48503302
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	BATF	chr12:48503228-48503587	GM12878	blood:	n/a	chr12:48503385-48503396 chr12:48503386-48503396
2	FOS	chr12:48503239-48503530	MCF10A-Er-Src	breast:	n/a	chr12:48503384-48503393 chr12:48503385-48503393 chr12:48503383-48503395 chr12:48503385-48503392 chr12:48503384-48503394
3	RUNX3	chr12:48503195-48503602	GM12878	blood:	n/a	n/a
4	JUND	chr12:48503251-48503545	HepG2	liver:	n/a	chr12:48503383-48503394 chr12:48503384-48503393 chr12:48503385-48503393 chr12:48503383-48503395 chr12:48503385-48503392 chr12:48503384-48503394
5	FOS	chr12:48503263-48503505	MCF10A-Er-Src	breast:	n/a	chr12:48503384-48503393 chr12:48503385-48503393 chr12:48503383-48503395 chr12:48503385-48503392 chr12:48503384-48503394
6	RUNX3	chr12:48503135-48503630	GM12878	blood:	n/a	chr12:48503185-48503194
7	FOS	chr12:48503285-48503560	MCF10A-Er-Src	breast:	n/a	chr12:48503384-48503393 chr12:48503385-48503393 chr12:48503383-48503395 chr12:48503385-48503392 chr12:48503384-48503394
8	BATF	chr12:48503275-48503534	GM12878	blood:	n/a	chr12:48503385-48503396 chr12:48503386-48503396
9	FOSL2	chr12:48503258-48503490	HepG2	liver:	n/a	chr12:48503384-48503393 chr12:48503385-48503393 chr12:48503383-48503395 chr12:48503385-48503392 chr12:48503384-48503394

No.	Distal block	Cell Line	Cell type
1	chr12:48502266..48504790-chr12:48510214..48512208,2	K562	blood:
2	chr12:48501965..48505279-chr12:48511816..48514639,4	K562	blood:
3	chr12:48495831..48503326-chr12:48548997..48555180,8	K562	blood:

Variant related genes	Relation type
SENP1	TF binding region
ENSG00000152556	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000258051	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1018973	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs10492080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783230	0.94[ASN][1000 genomes]
rs10783231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10783232	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10875751	0.90[ASN][1000 genomes]
rs11168451	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11168455	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11609399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612578	0.88[CEU][hapmap];0.96[JPT][hapmap]
rs11612970	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11613485	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11613781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12580764	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12581972	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12822085	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1476608	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1489111	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs17122565	0.95[JPT][hapmap]
rs17122611	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17122612	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17122613	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17122651	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1859441	0.86[CEU][hapmap];0.86[YRI][hapmap];0.80[EUR][1000 genomes]
rs1968071	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2258342	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2634699	0.82[CHB][hapmap]
rs2732455	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2732477	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2732487	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs3742074	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4075913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4141065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4293182	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4589362	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4760611	0.86[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs4760614	0.83[EUR][1000 genomes]
rs4760615	0.81[EUR][1000 genomes]
rs4760620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760677	0.83[EUR][1000 genomes]
rs4760683	0.87[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4760685	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4760692	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4760698	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs57054831	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57380031	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57655233	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58046797	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58331734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59766465	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60567660	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60681522	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6580651	0.83[EUR][1000 genomes]
rs6580653	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6580656	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6580660	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7133249	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs726354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72644842	0.83[EUR][1000 genomes]
rs72644843	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72644844	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72644845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72644846	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72644847	0.98[EUR][1000 genomes]
rs7296913	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7305418	0.85[CEU][hapmap]
rs7310579	0.81[EUR][1000 genomes]
rs7312326	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7315258	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7485057	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7485824	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs757556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7957764	0.81[EUR][1000 genomes]
rs7959755	0.94[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs7963934	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7967762	0.80[CEU][hapmap]
rs7969749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7971668	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs901964	0.86[CHB][hapmap];0.81[JPT][hapmap]

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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs879242	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48501000-48503600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:48501000-48504000	Weak transcription	Psoas Muscle	Psoas
3	chr12:48501000-48504200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:48501000-48504800	Weak transcription	Lung	lung
5	chr12:48501000-48508800	Weak transcription	K562	blood
6	chr12:48501200-48503400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:48501200-48503400	Weak transcription	Spleen	Spleen
8	chr12:48501200-48504600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:48501200-48512200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:48501400-48503800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:48501600-48506600	Weak transcription	Fetal Intestine Small	intestine
12	chr12:48502000-48503400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:48502000-48503800	Enhancers	GM12878-XiMat	blood
14	chr12:48503000-48504400	Enhancers	HMEC	breast
15	chr12:48503200-48503400	Enhancers	Hela-S3	cervix
16	chr12:48503200-48503400	Enhancers	HepG2	liver

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