Variant report

Variant	rs13027625
Chromosome Location	chr2:209057881-209057882
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	STAT3	chr2:209057620-209057956	MCF10A-Er-Src	breast:	n/a	chr2:209057837-209057848 chr2:209057816-209057827
2	STAT3	chr2:209057637-209057956	MCF10A-Er-Src	breast:	n/a	chr2:209057837-209057848 chr2:209057816-209057827
3	STAT1	chr2:209057303-209058285	Hela-S3	cervix:	n/a	chr2:209057816-209057827
4	STAT3	chr2:209057699-209057988	MCF10A-Er-Src	breast:	n/a	chr2:209057837-209057848 chr2:209057816-209057827
5	STAT3	chr2:209057650-209057972	MCF10A-Er-Src	breast:	n/a	chr2:209057837-209057848 chr2:209057816-209057827
6	IRF1	chr2:209057878-209058128	K562	blood:	n/a	n/a
7	STAT3	chr2:209057784-209057954	MCF10A-Er-Src	breast:	n/a	chr2:209057837-209057848 chr2:209057816-209057827
8	SRF	chr2:209057686-209057913	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
C2orf80	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10168933	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10192683	0.85[EUR][1000 genomes]
rs10432522	0.81[EUR][1000 genomes]
rs10445731	0.83[EUR][1000 genomes]
rs10445799	0.87[EUR][1000 genomes]
rs10445800	0.87[EUR][1000 genomes]
rs10932247	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10932248	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10932249	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10932250	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10932251	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12373811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12473347	0.83[EUR][1000 genomes]
rs13402685	1.00[ASN][1000 genomes]
rs13411179	0.89[EUR][1000 genomes]
rs13430046	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13432776	0.93[EUR][1000 genomes]
rs16840683	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2028878	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2197565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4675738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs4675740	0.83[EUR][1000 genomes]
rs4675741	0.83[EUR][1000 genomes]
rs6435428	0.83[EUR][1000 genomes]
rs6435429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6435431	0.83[EUR][1000 genomes]
rs6711758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6714981	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6740421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6743514	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6755619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs73065286	0.89[EUR][1000 genomes]
rs7585931	0.83[EUR][1000 genomes]
rs7588978	0.83[EUR][1000 genomes]
rs9967759	0.83[EUR][1000 genomes]
rs9967760	0.83[EUR][1000 genomes]
rs9967830	0.83[EUR][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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv584299	chr2:209021232-209067051	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv875749	chr2:209022909-209062388	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv875750	chr2:209022909-209069303	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv869592	chr2:209029861-209060862	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv2763083	chr2:209033581-209058397	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv875751	chr2:209042963-209110784	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	nsv522180	chr2:209052303-209062388	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv274878	chr2:209054297-209058385	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209040000-209064000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:209055000-209061000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:209055800-209064600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:209056600-209058600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:209057200-209058200	Enhancers	NHEK	skin
6	chr2:209057200-209058400	Enhancers	Stomach Mucosa	stomach
7	chr2:209057400-209058200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:209057400-209058200	Enhancers	Ovary	ovary
9	chr2:209057600-209058000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:209057600-209058400	Enhancers	Cortex derived primary cultured neurospheres	brain

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