Variant report

Variant	rs2864093
Chromosome Location	chr19:51975723-51975724
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:51975720-51975870	HA-sp	spinal cord:	n/a	n/a
2	TBL1XR1	chr19:51975689-51975806	K562	blood:	n/a	n/a
3	CTCF	chr19:51975680-51975830	AG10803	skin:	n/a	n/a
4	CUX1	chr19:51975639-51976560	K562	blood:	n/a	n/a
5	CTCF	chr19:51975680-51975830	HPAF	blood vessel:	n/a	n/a
6	CTCF	chr19:51975620-51975770	HL-60	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:51974430..51976310-chr19:52037889..52040847,2	K562	blood:
2	chr19:51975672..51976584-chr19:52164011..52164572,3	MCF-7	breast:
3	chr19:51974505..51976487-chr19:52010911..52013199,2	K562	blood:
4	chr19:51868665..51871642-chr19:51973620..51976713,3	K562	blood:

No data

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

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10424482	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10424572	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10424783	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10424804	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11878257	1.00[EUR][1000 genomes]
rs11878282	1.00[EUR][1000 genomes]
rs11878388	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11881105	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16982729	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17206902	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs185254	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2607257	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs2607258	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2607259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2607260	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28539101	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28607420	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2864090	1.00[EUR][1000 genomes]
rs2864091	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864092	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs36503	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56799568	0.87[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	0.89[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	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8101777	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8107537	0.87[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2864093	ZNF480	cis	cerebellum	SCAN
rs2864093	ZNF460	cis	parietal	SCAN

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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