Variant report

Variant	rs12475108
Chromosome Location	chr2:178538977-178538978
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178128784..178131655-chr2:178537635..178541213,3	K562	blood:
2	chr2:178128784..178131655-chr2:178537635..178540049,2	K562	blood:
3	chr1:67678579..67680079-chr2:178536885..178539298,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116044	Chromatin interaction
ENSG00000222043	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10167783	0.94[ASN][1000 genomes]
rs11678875	0.91[ASN][1000 genomes]
rs11682717	0.87[ASN][1000 genomes]
rs11890088	0.84[ASN][1000 genomes]
rs12467363	0.89[ASN][1000 genomes]
rs12469884	0.85[ASN][1000 genomes]
rs12471621	0.89[ASN][1000 genomes]
rs12611503	0.87[ASN][1000 genomes]
rs12612481	0.86[ASN][1000 genomes]
rs12616259	0.91[ASN][1000 genomes]
rs12990878	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12994392	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12997716	0.83[ASN][1000 genomes]
rs13008833	0.91[ASN][1000 genomes]
rs13008857	0.91[ASN][1000 genomes]
rs13009207	0.85[ASN][1000 genomes]
rs13034781	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1358328	0.94[ASN][1000 genomes]
rs1405714	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1405717	0.89[ASN][1000 genomes]
rs1405718	0.89[ASN][1000 genomes]
rs1527401	0.90[ASN][1000 genomes]
rs1527406	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1527407	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1544002	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2222711	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770005	0.93[ASN][1000 genomes]
rs3770007	0.93[ASN][1000 genomes]
rs3770008	0.86[ASN][1000 genomes]
rs3770009	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770010	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770011	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770012	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821006	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4144275	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4144276	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4337505	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4470372	0.91[ASN][1000 genomes]
rs4893838	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55792594	0.85[ASN][1000 genomes]
rs6433684	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7578325	0.93[ASN][1000 genomes]
rs7594362	0.86[ASN][1000 genomes]
rs7605493	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7605609	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7605757	0.93[ASN][1000 genomes]
rs880897	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs880898	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs880899	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv431812	chr2:178525371-178584470	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1007925	chr2:178535922-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv275124	chr2:178538584-178541159	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178531400-178540000	Weak transcription	K562	blood
2	chr2:178535000-178544800	Weak transcription	Right Atrium	heart
3	chr2:178535400-178540000	Weak transcription	Liver	Liver
4	chr2:178536000-178540000	Weak transcription	Brain Substantia Nigra	brain
5	chr2:178536000-178540000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:178536000-178544600	Weak transcription	Psoas Muscle	Psoas
7	chr2:178536200-178540200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:178536200-178540200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:178536600-178540400	Weak transcription	Fetal Stomach	stomach
10	chr2:178536600-178556000	Weak transcription	Pancreas	Pancrea
11	chr2:178537000-178540000	Weak transcription	Fetal Kidney	kidney
12	chr2:178537000-178540200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:178537200-178539600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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