Variant report

Variant	rs56131067
Chromosome Location	chr7:12633955-12633956
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	FOS	chr7:12633839-12634059	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr7:12633676-12634013	K562	blood:	n/a	n/a
3	POLR2A	chr7:12633781-12634288	K562	blood:	n/a	n/a
4	JUND	chr7:12633777-12634114	K562	blood:	n/a	n/a
5	MAZ	chr7:12633827-12634029	K562	blood:	n/a	n/a
6	MAFK	chr7:12633935-12634000	K562	blood:	n/a	n/a
7	FOS	chr7:12633814-12634095	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr7:12633801-12634084	MCF10A-Er-Src	breast:	n/a	n/a
9	CBX3	chr7:12633685-12634028	K562	blood:	n/a	n/a
10	IRF1	chr7:12633937-12634311	K562	blood:	n/a	n/a
11	FOS	chr7:12633791-12634114	MCF10A-Er-Src	breast:	n/a	n/a
12	RCOR1	chr7:12633738-12634088	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:12628422..12631395-chr7:12632472..12635866,3	K562	blood:

Variant related genes	Relation type
SCIN	TF binding region
ENSG00000006747	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1034856	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1118998	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11558844	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17283717	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17355921	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4458754	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55829483	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56085455	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57778115	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6967031	0.98[ASN][1000 genomes]
rs73060662	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73060664	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73060679	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73060680	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73062610	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73062611	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73062639	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7782451	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7799976	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7804260	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv1021371	chr7:12530491-12710429	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1017577	chr7:12530491-12722947	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1030764	chr7:12532287-12710429	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1020242	chr7:12605593-12641202	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3493690	chr7:12628257-12634980	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3493691	chr7:12628257-12634980	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv527833	chr7:12632085-12644502	Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56131067	SCIN	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12611800-12637600	Weak transcription	Colonic Mucosa	Colon
2	chr7:12625000-12645800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr7:12625000-12652000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr7:12625400-12667600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:12626200-12637400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:12628000-12635600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:12633400-12635000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:12633400-12635000	ZNF genes & repeats	Placenta	Placenta
9	chr7:12633600-12634800	Flanking Active TSS	K562	blood
10	chr7:12633800-12634000	Enhancers	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links