Variant report

Variant	rs28539101
Chromosome Location	chr19:51975027-51975028
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	CUX1	chr19:51974394-51975128	K562	blood:	n/a	n/a
2	MAFF	chr19:51974805-51975203	K562	blood:	n/a	chr19:51974997-51975015
3	MAFK	chr19:51974820-51975194	K562	blood:	n/a	chr19:51974999-51975014
4	MAFF	chr19:51974846-51975173	HepG2	liver:	n/a	chr19:51974997-51975015
5	ARID3A	chr19:51974344-51975047	K562	blood:	n/a	n/a
6	MAFK	chr19:51974831-51975187	HepG2	liver:	n/a	chr19:51974999-51975014
7	IRF1	chr19:51974349-51975179	K562	blood:	n/a	chr19:51974593-51974600
8	MAFK	chr19:51974830-51975184	IMR90	lung:	n/a	chr19:51974999-51975014
9	BACH1	chr19:51974820-51975214	K562	blood:	n/a	n/a
10	MAFK	chr19:51974863-51975184	HepG2	liver:	n/a	chr19:51974999-51975014
11	FOS	chr19:51974334-51975223	HUVEC	blood vessel:	n/a	chr19:51975004-51975015

No.	Distal block	Cell Line	Cell type
1	chr19:51974430..51976310-chr19:52037889..52040847,2	K562	blood:
2	chr19:51974505..51976487-chr19:52010911..52013199,2	K562	blood:
3	chr19:51868665..51871642-chr19:51973620..51976713,3	K562	blood:

Variant related genes	Relation type
SIGLEC26P	TF binding region
CEACAM18	TF binding region
ENSG00000269403	Chromatin interaction
ENSG00000105379	Chromatin interaction
ENSG00000269580	Chromatin interaction
ENSG00000268520	Chromatin interaction
ENSG00000160318	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10424482	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10424572	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10424783	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10424804	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11878257	1.00[EUR][1000 genomes]
rs11878282	1.00[EUR][1000 genomes]
rs11878388	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11881105	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16982729	0.98[EUR][1000 genomes]
rs17206902	1.00[EUR][1000 genomes]
rs185254	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2607257	1.00[EUR][1000 genomes]
rs2607258	1.00[EUR][1000 genomes]
rs2607259	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2607260	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28607420	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2864090	1.00[EUR][1000 genomes]
rs2864091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864092	1.00[EUR][1000 genomes]
rs2864093	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36501	0.84[AFR][1000 genomes]
rs36503	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56799568	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61201251	0.98[EUR][1000 genomes]
rs62115066	0.98[EUR][1000 genomes]
rs62116369	1.00[EUR][1000 genomes]
rs62116370	1.00[EUR][1000 genomes]
rs62116371	1.00[EUR][1000 genomes]
rs62116417	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62116418	0.87[EUR][1000 genomes]
rs62116419	0.87[EUR][1000 genomes]
rs62116420	0.87[EUR][1000 genomes]
rs62116422	0.87[EUR][1000 genomes]
rs7246811	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8101777	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8107537	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][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	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers 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 miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv458724	chr19:51925519-51975723	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv579965	chr19:51925519-51975723	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv961163	chr19:51971394-51976393	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51972000-51976000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr19:51972600-51976400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr19:51974800-51976000	Enhancers	K562	blood
4	chr19:51975000-51976600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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