Variant report

Variant	rs12700778
Chromosome Location	chr7:3339352-3339353
allele	C/G
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	CTCF	chr7:3339276-3341235	SK-N-SH	brain:	n/a	chr7:3339295-3339303 chr7:3340483-3340496 chr7:3339382-3339390
2	SMC3	chr7:3339220-3341228	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr7:3339138-3341287	SK-N-SH	brain:	n/a	chr7:3339313-3339327 chr7:3339322-3339335
4	POLR2A	chr7:3339196-3339590	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:3254030..3256348-chr7:3338235..3340171,2	MCF-7	breast:

Variant related genes	Relation type
SDK1	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11766873	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11770645	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11983024	0.91[ASN][1000 genomes]
rs12234397	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12700775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12700776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700780	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133257	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2334058	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34368704	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34469526	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35888267	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36089007	0.89[ASN][1000 genomes]
rs36094267	0.92[EUR][1000 genomes]
rs4348387	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62437660	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62437661	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62437662	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62437663	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62437664	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440294	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62440295	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62441387	0.92[EUR][1000 genomes]
rs72576953	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72576955	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72576957	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464264	chr7:3194156-3349625	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv605880	chr7:3194156-3349625	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1023127	chr7:3216344-3466223	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2758100	chr7:3286625-3560229	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv2759500	chr7:3286625-3560229	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1019515	chr7:3300048-3479972	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv887324	chr7:3308195-3400105	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv1803572	chr7:3327994-3341589	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv605885	chr7:3337081-3340551	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3334800-3339600	Weak transcription	Pancreas	Pancrea
2	chr7:3335000-3340000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:3337600-3339800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:3338200-3339400	Enhancers	Adipose Nuclei	Adipose
5	chr7:3338400-3339400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:3338600-3339600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:3338600-3340200	Enhancers	NHDF-Ad	bronchial
8	chr7:3339000-3339400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:3339000-3339800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr7:3339200-3339800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:3339200-3339800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:3339200-3340000	Bivalent Enhancer	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links