Variant report

Variant	rs57478994
Chromosome Location	chr1:93486926-93486927
allele	A/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	CTCF	chr1:93486758-93487621	SK-N-SH	brain:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
2	STAT3	chr1:93486918-93487360	MCF10A-Er-Src	breast:	n/a	n/a
3	SMC3	chr1:93486859-93487534	SK-N-SH	brain:	n/a	n/a
4	RAD21	chr1:93486875-93487832	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:93485980..93488495-chr1:93489742..93491453,2	K562	blood:
2	chr1:93486773..93487911-chr1:93527469..93528398,9	K562	blood:
3	chr1:93486837..93487799-chr1:94374760..94375360,2	K562	blood:
4	chr1:93485808..93487588-chr1:93526047..93528280,2	MCF-7	breast:
5	chr1:93486832..93487777-chr1:93527684..93528337,5	MCF-7	breast:
6	chr1:93324004..93325373-chr1:93486850..93487700,5	K562	blood:

Variant related genes	Relation type
RN7SKP123	TF binding region
ENSG00000023909	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11164860	0.84[ASN][1000 genomes]
rs11164861	0.89[ASN][1000 genomes]
rs12022729	0.99[ASN][1000 genomes]
rs12023767	0.99[ASN][1000 genomes]
rs12027025	0.99[ASN][1000 genomes]
rs12039256	0.99[ASN][1000 genomes]
rs12043577	0.99[ASN][1000 genomes]
rs12119421	0.98[ASN][1000 genomes]
rs12130551	0.89[ASN][1000 genomes]
rs12134501	0.99[ASN][1000 genomes]
rs12141895	0.99[ASN][1000 genomes]
rs1678778	0.95[ASN][1000 genomes]
rs2086312	0.87[ASN][1000 genomes]
rs2253595	0.91[ASN][1000 genomes]
rs2492898	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2928183	0.88[ASN][1000 genomes]
rs4626900	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4847227	0.96[ASN][1000 genomes]
rs485336	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs486370	0.88[ASN][1000 genomes]
rs492054	0.84[ASN][1000 genomes]
rs492754	0.84[ASN][1000 genomes]
rs496465	0.84[ASN][1000 genomes]
rs497540	0.85[ASN][1000 genomes]
rs504418	0.95[ASN][1000 genomes]
rs517856	0.97[ASN][1000 genomes]
rs521527	0.95[ASN][1000 genomes]
rs524045	1.00[ASN][1000 genomes]
rs536837	0.83[ASN][1000 genomes]
rs544051	0.81[ASN][1000 genomes]
rs544285	0.81[ASN][1000 genomes]
rs553396	0.85[ASN][1000 genomes]
rs557812	0.93[ASN][1000 genomes]
rs56320266	0.88[ASN][1000 genomes]
rs572131	0.88[ASN][1000 genomes]
rs590296	0.95[ASN][1000 genomes]
rs591820	0.85[ASN][1000 genomes]
rs591868	0.85[ASN][1000 genomes]
rs592751	0.85[ASN][1000 genomes]
rs61523335	0.85[AFR][1000 genomes]
rs638462	0.82[ASN][1000 genomes]
rs638958	0.81[ASN][1000 genomes]
rs664524	0.93[ASN][1000 genomes]
rs664852	0.94[ASN][1000 genomes]
rs6674738	0.84[ASN][1000 genomes]
rs680285	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808833	0.98[ASN][1000 genomes]
rs9787147	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870775	chr1:93481640-93543119	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93474200-93490600	Weak transcription	K562	blood
2	chr1:93480400-93491000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:93482200-93487400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:93482400-93487000	Weak transcription	Liver	Liver
5	chr1:93482600-93487400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:93486800-93494000	Enhancers	Dnd41	blood

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