Variant report

Variant	rs2864108
Chromosome Location	chr19:52073911-52073912
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	YY1	chr19:52073863-52074823	A549	lung:	n/a	chr19:52074309-52074321
2	ZMIZ1	chr19:52073811-52074656	K562	blood:	n/a	n/a
3	YY1	chr19:52073821-52074894	SK-N-SH	brain:	n/a	chr19:52074309-52074321
4	HCFC1	chr19:52073817-52075083	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr19:52073855-52074657	GM12878	blood:	n/a	n/a
6	IRF1	chr19:52073836-52074839	K562	blood:	n/a	n/a
7	YY1	chr19:52073802-52074740	SK-N-SH_RA	brain:	n/a	chr19:52074309-52074321
8	YY1	chr19:52073909-52074858	GM12878	blood:	n/a	chr19:52074309-52074321
9	YY1	chr19:52073872-52074873	SK-N-SH_RA	brain:	n/a	chr19:52074309-52074321
10	EP300	chr19:52073591-52074538	K562	blood:	n/a	chr19:52074518-52074525
11	YY1	chr19:52073815-52074789	K562	blood:	n/a	chr19:52074309-52074321
12	YY1	chr19:52073910-52074890	A549	lung:	n/a	chr19:52074309-52074321
13	CUX1	chr19:52073824-52074715	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52067924..52069663-chr19:52072796..52074463,2	MCF-7	breast:
2	chr19:51970546..51972983-chr19:52071317..52074312,2	K562	blood:
3	chr19:52008446..52010524-chr19:52071337..52074269,2	K562	blood:
4	chr19:52073774..52076492-chr19:52083212..52084974,2	K562	blood:
5	chr19:52073066..52077206-chr19:52096074..52099799,4	K562	blood:

Variant related genes	Relation type
ZNF175	TF binding region
ENSG00000268839	Chromatin interaction
ENSG00000167765	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000268267	Chromatin interaction
ENSG00000105497	Chromatin interaction
ENSG00000268957	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1379284	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1585160	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16982846	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17453522	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305371	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864106	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2864109	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3752132	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6509552	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7245838	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7249641	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8108872	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8111685	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2864108	ZNF175	cis	Esophagus Muscularis	GTEx
rs2864108	ZNF175	cis	Artery Tibial	GTEx
rs2864108	ZNF175	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52069400-52074000	Weak transcription	GM12878-XiMat	blood
2	chr19:52070200-52074200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:52071200-52074000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr19:52071400-52074200	Weak transcription	Placenta	Placenta
5	chr19:52073200-52074400	Weak transcription	Pancreas	Pancrea
6	chr19:52073400-52074000	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr19:52073400-52074000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr19:52073400-52074000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:52073600-52074000	Flanking Active TSS	K562	blood
10	chr19:52073800-52074000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:52073800-52074000	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr19:52073800-52074000	Bivalent/Poised TSS	Primary B cells from cord blood	blood
13	chr19:52073800-52074000	Enhancers	Primary T cells from cord blood	blood
14	chr19:52073800-52074000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:52073800-52074000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:52073800-52074000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr19:52073800-52074000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr19:52073800-52074000	Flanking Active TSS	Thymus	Thymus
19	chr19:52073800-52074200	Enhancers	Primary B cells from peripheral blood	blood
20	chr19:52073800-52074200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr19:52073800-52074200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:52073800-52074200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr19:52073800-52074400	Flanking Active TSS	Dnd41	blood
24	chr19:52073800-52075000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:52073800-52075000	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr19:52073800-52075200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:52073800-52075400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr19:52073800-52075800	Active TSS	A549	lung

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