Variant report

Variant	rs2864109
Chromosome Location	chr19:52076133-52076134
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	FOS	chr19:52075387-52077326	HUVEC	blood vessel:	n/a	n/a
2	GATA2	chr19:52075754-52077117	HUVEC	blood vessel:	n/a	chr19:52075825-52075835 chr19:52076736-52076745 chr19:52076927-52076934 chr19:52076831-52076840
3	POLR2A	chr19:52074025-52077434	U87	brain:	n/a	n/a
4	FOSL2	chr19:52076032-52076550	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr19:52075274-52077228	HUVEC	blood vessel:	n/a	n/a
6	CEBPB	chr19:52075787-52076153	K562	blood:	n/a	n/a
7	CEBPB	chr19:52075837-52076906	IMR90	lung:	n/a	n/a
8	RCOR1	chr19:52074190-52076188	K562	blood:	n/a	n/a
9	POLR2A	chr19:52074059-52077284	PBDE	blood:	n/a	n/a
10	BHLHE40	chr19:52075562-52076309	K562	blood:	n/a	n/a
11	SPI1	chr19:52075558-52076183	HL-60	blood:	n/a	n/a
12	GATA1	chr19:52074810-52077148	PBDE	blood:	n/a	chr19:52075825-52075835 chr19:52074842-52074853 chr19:52076736-52076745 chr19:52076927-52076934 chr19:52076831-52076840
13	POLR2A	chr19:52074872-52077276	U87	brain:	n/a	n/a
14	POLR2A	chr19:52074937-52076991	HUVEC	blood vessel:	n/a	n/a
15	MYC	chr19:52075565-52076136	K562	blood:	n/a	n/a
16	CBX3	chr19:52075623-52076142	K562	blood:	n/a	n/a
17	TEAD4	chr19:52074869-52076257	K562	blood:	n/a	n/a
18	POLR2A	chr19:52075327-52076974	HUVEC	blood vessel:	n/a	n/a
19	IRF1	chr19:52075356-52076395	K562	blood:	n/a	n/a
20	POLR2A	chr19:52074069-52077434	U87	brain:	n/a	n/a
21	POLR2A	chr19:52074872-52077594	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52075666..52078013-chr19:52102124..52103680,2	K562	blood:
2	chr19:52073774..52076492-chr19:52083212..52084974,2	K562	blood:
3	chr19:52073066..52077206-chr19:52096074..52099799,4	K562	blood:

Variant related genes	Relation type
ZNF175	TF binding region
ENSG00000167765	Chromatin interaction
ENSG00000267808	Chromatin interaction
ENSG00000105497	Chromatin interaction
ENSG00000269388	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1125620	0.92[ASN][1000 genomes]
rs1379284	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1585160	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16982846	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453522	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1962189	0.93[ASN][1000 genomes]
rs2305371	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2864106	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864108	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3752132	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308054	0.90[ASN][1000 genomes]
rs6509552	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7245838	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249641	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8102214	0.92[ASN][1000 genomes]
rs8108872	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111685	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv579966	chr19:52075622-52131119	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2864109	ZNF175	Cis_1M	lymphoblastoid	RTeQTL
rs2864109	ZNF175	cis	Esophagus Muscularis	GTEx
rs2864109	ZNF175	cis	Esophagus Mucosa	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52074800-52077400	Flanking Active TSS	HUVEC	blood vessel
2	chr19:52075000-52076200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:52075000-52076200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:52075000-52076200	Flanking Active TSS	NHLF	lung
5	chr19:52075000-52076400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr19:52075000-52076800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:52075000-52077000	Flanking Active TSS	Osteobl	bone
8	chr19:52075200-52076200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr19:52075200-52076200	Flanking Active TSS	NH-A	brain
10	chr19:52075200-52076400	Enhancers	Primary B cells from peripheral blood	blood
11	chr19:52075200-52076400	Enhancers	Small Intestine	intestine
12	chr19:52075200-52076400	Flanking Active TSS	NHDF-Ad	bronchial
13	chr19:52075200-52077000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:52075400-52076200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr19:52075400-52076200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:52075400-52076200	Enhancers	Brain Substantia Nigra	brain
17	chr19:52075400-52076200	Enhancers	Placenta	Placenta
18	chr19:52075400-52076200	Enhancers	Fetal Stomach	stomach
19	chr19:52075400-52076400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:52075400-52076400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:52075400-52076400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr19:52075400-52076400	Enhancers	Spleen	Spleen
23	chr19:52075400-52076600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:52075400-52076600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:52075400-52076800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:52075400-52084600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:52075400-52087400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr19:52075400-52090200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:52075600-52076200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:52075600-52076200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:52075600-52076200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:52075600-52076200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr19:52075600-52076200	Enhancers	Fetal Heart	heart
34	chr19:52075600-52076200	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr19:52075600-52076400	Weak transcription	Primary T cells from cord blood	blood
36	chr19:52075600-52076400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:52075600-52076400	Weak transcription	Esophagus	oesophagus
38	chr19:52075600-52076400	Weak transcription	Fetal Intestine Large	intestine
39	chr19:52075600-52076600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr19:52075600-52076600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr19:52075600-52076600	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr19:52075600-52076600	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr19:52075600-52076600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr19:52075600-52076600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr19:52075600-52076800	Enhancers	Colon Smooth Muscle	Colon
46	chr19:52075600-52076800	Enhancers	Right Atrium	heart
47	chr19:52075600-52084400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr19:52075600-52084400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:52075600-52084600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:52075600-52084600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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