Variant report

Variant	rs7744579
Chromosome Location	chr6:70931426-70931427
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	NFIC	chr6:70930950-70931434	HepG2	liver:	n/a	n/a
2	SPI1	chr6:70931243-70931606	HL-60	blood:	n/a	chr6:70931436-70931445 chr6:70931433-70931446 chr6:70931437-70931444 chr6:70931434-70931447
3	CTCF	chr6:70930344-70931590	SK-N-SH	brain:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
4	SMC3	chr6:70930565-70931507	SK-N-SH	brain:	n/a	chr6:70930845-70930859
5	SPI1	chr6:70931266-70931578	HL-60	blood:	n/a	chr6:70931436-70931445 chr6:70931433-70931446 chr6:70931437-70931444 chr6:70931434-70931447
6	RAD21	chr6:70930276-70931857	SK-N-SH	brain:	n/a	chr6:70930844-70930863 chr6:70930846-70930853

No.	Distal block	Cell Line	Cell type
1	chr6:70931382..70931981-chr6:71593939..71594756,2	MCF-7	breast:
2	chr6:70930597..70933117-chr6:70988758..70990429,2	K562	blood:
3	chr6:70930581..70931580-chr6:71078690..71079470,4	MCF-7	breast:
4	chr6:70930172..70932460-chr6:71107052..71108700,2	K562	blood:

Variant related genes	Relation type
ENSG00000253809	TF binding region
ENSG00000112280	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1200568	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1212491	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12192985	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12201251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1474044	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1517041	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1517044	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs1517045	0.89[EUR][1000 genomes]
rs1616745	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16868775	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1753258	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2676613	0.94[ASN][1000 genomes]
rs3793071	0.84[CHD][hapmap]
rs3806053	0.89[EUR][1000 genomes]
rs3806066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707705	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4707706	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs476863	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs529805	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs540152	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs552628	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[ASN][1000 genomes]
rs556270	0.96[ASN][1000 genomes]
rs591365	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs591421	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs595957	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs622566	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs627540	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs662828	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs671910	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6909142	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7739562	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs802172	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs802173	0.82[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[ASN][1000 genomes]
rs802174	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs802175	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs802176	0.94[ASN][1000 genomes]
rs802178	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs802180	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs802182	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs802184	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs802185	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs802187	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs802188	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs802189	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9346371	0.82[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9346372	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9454994	0.83[EUR][1000 genomes]
rs997953	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026151	chr6:70621616-70946967	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv933674	chr6:70663616-70973112	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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
5	nsv830683	chr6:70743422-70941190	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7744579	MTO1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70930000-70932000	Enhancers	Duodenum Mucosa	Duodenum
2	chr6:70930200-70931600	Enhancers	Stomach Mucosa	stomach
3	chr6:70930200-70931800	Enhancers	Fetal Intestine Small	intestine
4	chr6:70930200-70932200	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr6:70930400-70932200	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr6:70930800-70931800	Enhancers	Liver	Liver
7	chr6:70931000-70931600	Flanking Active TSS	HepG2	liver
8	chr6:70931200-70931800	Enhancers	Fetal Intestine Large	intestine
9	chr6:70931200-70932000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:70931400-70931600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:70931400-70932400	Enhancers	Brain Germinal Matrix	brain
12	chr6:70931400-70934800	Weak transcription	Brain Substantia Nigra	brain
13	chr6:70931400-70961400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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