Variant report

Variant	rs60254449
Chromosome Location	chr12:49756621-49756622
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr12:49756513-49756674	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49721808..49725568-chr12:49752625..49757232,4	MCF-7	breast:
2	chr12:49737926..49740878-chr12:49754059..49756670,2	MCF-7	breast:
3	chr12:49755123..49759398-chr12:49960657..49963861,3	MCF-7	breast:
4	chr12:49754738..49757978-chr12:49758719..49762936,8	K562	blood:
5	chr12:49739210..49743627-chr12:49754330..49757005,4	MCF-7	breast:
6	chr12:49755189..49756815-chr12:49905367..49908024,2	K562	blood:

No data

Variant related genes	Relation type
SPATS2	TF binding region
ENSG00000110844	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000178401	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11169055	1.00[AMR][1000 genomes]
rs11830622	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11834883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11836969	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12296998	1.00[AMR][1000 genomes]
rs12298123	1.00[AMR][1000 genomes]
rs12298506	1.00[AMR][1000 genomes]
rs12300085	1.00[AMR][1000 genomes]
rs12306942	1.00[AMR][1000 genomes]
rs12309399	1.00[AMR][1000 genomes]
rs12310046	1.00[AMR][1000 genomes]
rs12311319	1.00[AMR][1000 genomes]
rs12311910	1.00[AMR][1000 genomes]
rs12313583	1.00[AMR][1000 genomes]
rs12314348	1.00[AMR][1000 genomes]
rs12315746	1.00[AMR][1000 genomes]
rs12315941	1.00[AMR][1000 genomes]
rs12318913	1.00[AMR][1000 genomes]
rs12320104	1.00[AMR][1000 genomes]
rs12320434	1.00[AMR][1000 genomes]
rs12320612	1.00[AMR][1000 genomes]
rs12321717	1.00[AMR][1000 genomes]
rs13377828	1.00[AMR][1000 genomes]
rs57970210	1.00[AMR][1000 genomes]
rs58867453	1.00[AMR][1000 genomes]
rs59250711	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59570650	1.00[AMR][1000 genomes]
rs60507124	1.00[AMR][1000 genomes]
rs60658484	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61227990	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
6	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49753000-49758000	Weak transcription	HUVEC	blood vessel
2	chr12:49753000-49758400	Weak transcription	NHLF	lung
3	chr12:49753000-49758800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:49753000-49759400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:49753000-49759600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr12:49753200-49758600	Weak transcription	Osteobl	bone
7	chr12:49753200-49758800	Weak transcription	Hela-S3	cervix
8	chr12:49753400-49758200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:49753400-49758600	Weak transcription	HMEC	breast
10	chr12:49753400-49758800	Weak transcription	HepG2	liver
11	chr12:49753800-49758200	Weak transcription	NHEK	skin
12	chr12:49753800-49758400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:49753800-49758400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:49753800-49758600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:49754000-49758200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:49754200-49757800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:49754200-49758400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:49755600-49757800	Weak transcription	A549	lung

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