Variant report

Variant	rs12474854
Chromosome Location	chr2:10897512-10897513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10891179..10894114-chr2:10896101..10897894,3	MCF-7	breast:
2	chr2:10897264..10897998-chr2:10917360..10918173,2	MCF-7	breast:
3	chr2:10897105..10899038-chr2:10904110..10905856,2	MCF-7	breast:
4	chr2:10897348..10898187-chr2:10917680..10918180,2	MCF-7	breast:
5	chr2:10860581..10862851-chr2:10897121..10899089,2	MCF-7	breast:
6	chr2:10897186..10898231-chr2:10913937..10914521,3	MCF-7	breast:
7	chr2:10897383..10898321-chr2:10917276..10918707,4	MCF-7	breast:
8	chr2:10897188..10898025-chr2:11638492..11639157,2	MCF-7	breast:
9	chr2:10897188..10898301-chr2:11638390..11639400,5	MCF-7	breast:
10	chr2:10863130..10866281-chr2:10896186..10898576,3	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10929697	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12467545	0.90[EUR][1000 genomes]
rs12473683	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16856603	0.91[EUR][1000 genomes]
rs16856608	0.90[EUR][1000 genomes]
rs2171776	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28623106	0.91[EUR][1000 genomes]
rs2884288	1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs4669624	0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57017343	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58364209	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59337562	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59676698	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60925909	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61642673	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62128992	0.91[EUR][1000 genomes]
rs67490022	0.88[EUR][1000 genomes]
rs72777372	0.91[EUR][1000 genomes]
rs7573590	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000953	chr2:10717304-10921805	Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv535584	chr2:10717304-10921805	Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv833381	chr2:10723465-10911284	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1000731	chr2:10758657-10943882	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12474854	C2orf50	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10883000-10899400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:10892600-10899000	Weak transcription	Fetal Intestine Small	intestine
3	chr2:10892600-10899200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr2:10892600-10905400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:10893000-10897600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:10896000-10897600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:10896000-10899400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:10896000-10899600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:10896000-10902800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:10896800-10897800	Weak transcription	Placenta	Placenta
11	chr2:10897400-10897600	Bivalent Enhancer	HepG2	liver
12	chr2:10897400-10902400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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