Variant report

Variant	rs7245838
Chromosome Location	chr19:52074366-52074367
allele	G/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	SIN3AK20	chr19:52074338-52074639	PFSK-1	brain:	n/a	n/a
2	EBF1	chr19:52074261-52074568	GM12878	blood:	n/a	n/a
3	ATF2	chr19:52074106-52074660	GM12878	blood:	n/a	n/a
4	TEAD4	chr19:52074238-52074685	HepG2	liver:	n/a	chr19:52074268-52074277
5	YY1	chr19:52073915-52074690	GM12892	blood:	n/a	chr19:52074309-52074321
6	GTF2F1	chr19:52074274-52074578	K562	blood:	n/a	n/a
7	MYC	chr19:52074217-52074615	MCF10A-Er-Src	breast:	n/a	n/a
8	GABPA	chr19:52074258-52074894	HL-60	blood:	n/a	chr19:52074457-52074471 chr19:52074460-52074474 chr19:52074460-52074471
9	POLR2A	chr19:52074162-52074835	K562	blood:	n/a	n/a
10	RFX5	chr19:52074286-52074680	GM12878	blood:	n/a	n/a
11	PML	chr19:52074172-52074760	K562	blood:	n/a	n/a
12	TBP	chr19:52074094-52074697	K562	blood:	n/a	n/a
13	FOXM1	chr19:52074189-52074713	GM12878	blood:	n/a	n/a
14	TCF12	chr19:52074231-52074505	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr19:52074297-52074786	PANC-1	pancreas:	n/a	n/a
16	HEY1	chr19:52074361-52074728	HepG2	liver:	n/a	n/a
17	TBL1XR1	chr19:52074185-52074610	GM12878	blood:	n/a	n/a
18	RCOR1	chr19:52074217-52074513	HepG2	liver:	n/a	n/a
19	RCOR1	chr19:52074083-52074616	GM12878	blood:	n/a	n/a
20	RELA	chr19:52074187-52074749	GM19099	blood:	n/a	n/a
21	SIX5	chr19:52074067-52074819	A549	lung:	n/a	n/a
22	MAX	chr19:52074185-52074682	K562	blood:	n/a	n/a
23	POLR2A	chr19:52074326-52074714	Hela-S3	cervix:	n/a	n/a
24	BCL3	chr19:52074184-52074769	A549	lung:	n/a	chr19:52074479-52074487 chr19:52074517-52074526
25	PML	chr19:52074274-52074608	GM12878	blood:	n/a	n/a
26	YY1	chr19:52074019-52074684	HepG2	liver:	n/a	chr19:52074309-52074321
27	TEAD4	chr19:52074320-52074774	ECC-1	luminal epithelium:	n/a	n/a
28	MAX	chr19:52074074-52074932	A549	lung:	n/a	n/a
29	ETS1	chr19:52074077-52074712	A549	lung:	n/a	chr19:52074516-52074525 chr19:52074513-52074529 chr19:52074517-52074526 chr19:52074515-52074524 chr19:52074517-52074526 chr19:52074518-52074528 chr19:52074517-52074528 chr19:52074517-52074526 chr19:52074514-52074527 chr19:52074517-52074526 chr19:52074517-52074526 chr19:52074517-52074526 chr19:52074517-52074526
30	YY1	chr19:52073950-52074902	SK-N-SH	brain:	n/a	chr19:52074309-52074321
31	YY1	chr19:52073863-52074823	A549	lung:	n/a	chr19:52074309-52074321
32	HEY1	chr19:52074151-52074648	K562	blood:	n/a	n/a
33	MAFK	chr19:52074105-52074641	K562	blood:	n/a	n/a
34	ELK1	chr19:52074128-52074673	K562	blood:	n/a	chr19:52074517-52074526 chr19:52074517-52074526
35	SETDB1	chr19:52074250-52074591	U2OS	brain:	n/a	n/a
36	CREB1	chr19:52074176-52074734	K562	blood:	n/a	n/a
37	MYC	chr19:52074214-52074614	MCF10A-Er-Src	breast:	n/a	n/a
38	NR2F2	chr19:52074045-52075159	K562	blood:	n/a	n/a
39	NRF1	chr19:52074363-52074591	HepG2	liver:	n/a	chr19:52074457-52074471 chr19:52074459-52074470 chr19:52074460-52074474 chr19:52074460-52074471
40	ARID3A	chr19:52074201-52074534	HepG2	liver:	n/a	n/a
41	CHD1	chr19:52074193-52074853	GM12878	blood:	n/a	n/a
42	ELF1	chr19:52074212-52074792	K562	blood:	n/a	chr19:52074516-52074525 chr19:52074513-52074526 chr19:52074515-52074526 chr19:52074515-52074526
43	BRCA1	chr19:52074249-52074643	GM12878	blood:	n/a	chr19:52074547-52074554
44	USF1	chr19:52074152-52074754	A549	lung:	n/a	n/a
45	SIX5	chr19:52074149-52074673	GM12878	blood:	n/a	n/a
46	SIX5	chr19:52073945-52074824	A549	lung:	n/a	n/a
47	THAP1	chr19:52074239-52074683	K562	blood:	n/a	chr19:52074416-52074440
48	POLR2A	chr19:52074352-52074750	A549	lung:	n/a	n/a
49	SPI1	chr19:52074175-52074731	HL-60	blood:	n/a	chr19:52074513-52074526
50	MTA3	chr19:52074163-52075563	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:52074348-52074398	AG09319	gingival:	n/a
2	chr19:52074318-52074368	HMEC	breast:	n/a
3	chr19:52074318-52074368	HRCEpiC	kidney:	n/a
4	chr19:52074318-52074368	HCF	heart:	n/a
5	chr19:52074318-52074368	HepG2	liver:	n/a
6	chr19:52074318-52074368	GM12891	blood:	n/a
7	chr19:52074318-52074368	GM12878	blood:	n/a
8	chr19:52074348-52074398	AoSMC	blood vessel:	n/a
9	chr19:52074348-52074398	BE2_C	brain:	n/a
10	chr19:52074348-52074398	NH-A	brain:	n/a
11	chr19:52074318-52074368	SKMC	muscle:	n/a
12	chr19:52074318-52074368	HEK293	kidney:	embryo
13	chr19:52074348-52074398	HRPEpiC	eye:	n/a
14	chr19:52074318-52074368	SK-N-SH_RA	brain:	n/a
15	chr19:52074348-52074398	RPTEC	kidney:	n/a
16	chr19:52074348-52074398	AG04450	lung:	fetal
17	chr19:52074348-52074398	HRCEpiC	kidney:	n/a
18	chr19:52074348-52074398	HMEC	breast:	n/a
19	chr19:52074318-52074368	AG04449	skin:	fetal
20	chr19:52074318-52074368	AG09319	gingival:	n/a
21	chr19:52074318-52074368	ECC-1	luminal epithelium:	n/a
22	chr19:52074318-52074368	NHBE	bronchial:	n/a
23	chr19:52074318-52074368	Jurkat	blood:	n/a
24	chr19:52074348-52074398	PFSK-1	brain:	n/a
25	chr19:52074348-52074398	HEK293	kidney:	embryo
26	chr19:52074348-52074398	LNCaP	prostate:	n/a
27	chr19:52074318-52074368	NH-A	brain:	n/a
28	chr19:52074318-52074368	A549	lung:	n/a
29	chr19:52074348-52074398	Caco-2	colon:	n/a
30	chr19:52074318-52074368	HPAEpiC	pulmonary alveolar:	n/a
31	chr19:52074348-52074398	NB4	blood:	n/a
32	chr19:52074318-52074368	HRPEpiC	eye:	n/a
33	chr19:52074348-52074398	HepG2	liver:	n/a
34	chr19:52074318-52074368	ovcar-3	ovarian:	n/a
35	chr19:52074348-52074398	SK-N-MC	brain:	n/a
36	chr19:52074318-52074368	HUVEC	blood vessel:	n/a
37	chr19:52074318-52074368	U87	brain:	n/a
38	chr19:52074318-52074368	HL-60	blood:	n/a
39	chr19:52074348-52074398	GM12878	blood:	n/a
40	chr19:52074348-52074398	ECC-1	luminal epithelium:	n/a
41	chr19:52074348-52074398	T-47D	breast:	n/a
42	chr19:52074318-52074368	NB4	blood:	n/a
43	chr19:52074318-52074368	HEEpiC	esophagus:	n/a
44	chr19:52074318-52074368	Caco-2	colon:	n/a
45	chr19:52074348-52074398	Jurkat	blood:	n/a
46	chr19:52074318-52074368	AoSMC	blood vessel:	n/a
47	chr19:52074318-52074368	H1-hESC	embryonic stem cell:	embryo
48	chr19:52074318-52074368	HCT-116	colon:	n/a
49	chr19:52074348-52074398	HNPCEpiC	eye:	n/a
50	chr19:52074318-52074368	SK-N-SH	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52067924..52069663-chr19:52072796..52074463,2	MCF-7	breast:
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
ZNF175	CpG island
ENSG00000105497	Chromatin interaction
ENSG00000167765	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000268267	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1125620	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1379284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1585160	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16982846	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453522	0.95[CEU][hapmap];0.94[JPT][hapmap];0.99[EUR][1000 genomes]
rs1962189	0.83[JPT][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2305371	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2864106	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864108	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2864109	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs3752132	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308054	0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6509552	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7249641	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8102214	0.86[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs8108872	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111685	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7245838	ZNF175	cis	Lymphoblastoid	GTEx
rs7245838	ZNF175	cis	Esophagus Muscularis	GTEx
rs7245838	ZNF175	cis	Esophagus Mucosa	GTEx
rs7245838	TNNI3	cis	cerebellum	SCAN
rs7245838	ZNF175	cis	multi-tissue	Pritchard
rs7245838	ZNF544	cis	parietal	SCAN
rs7245838	SBK2	cis	cerebellum	SCAN
rs7245838	ZNF71	cis	cerebellum	SCAN
rs7245838	ZNF175	cis	lymphoblastoid	seeQTL
rs7245838	ZNF175	Cis_1M	lymphoblastoid	RTeQTL
rs7245838	FCAR	cis	parietal	SCAN
rs7245838	ZNF808	cis	parietal	SCAN
rs7245838	ENSG00000105497	cis	multi-tissue	Pritchard

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52073200-52074400	Weak transcription	Pancreas	Pancrea
2	chr19:52073800-52074400	Flanking Active TSS	Dnd41	blood
3	chr19:52073800-52075000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:52073800-52075000	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr19:52073800-52075200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:52073800-52075400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr19:52073800-52075800	Active TSS	A549	lung
8	chr19:52074000-52074400	Active TSS	Primary T cells fromperipheralblood	blood
9	chr19:52074000-52074400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:52074000-52074400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr19:52074000-52074400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr19:52074000-52074600	Active TSS	Primary B cells from cord blood	blood
13	chr19:52074000-52074600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr19:52074000-52074600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr19:52074000-52074800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr19:52074000-52074800	Active TSS	Primary hematopoietic stem cells	blood
17	chr19:52074000-52074800	Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr19:52074000-52074800	Active TSS	Adipose Nuclei	Adipose
19	chr19:52074000-52074800	Active TSS	Liver	Liver
20	chr19:52074000-52074800	Active TSS	Thymus	Thymus
21	chr19:52074000-52074800	Active TSS	Monocytes-CD14+_RO01746	blood
22	chr19:52074000-52075000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:52074000-52075000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:52074000-52075000	Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr19:52074000-52075000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:52074000-52075000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:52074000-52075000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:52074000-52075000	Active TSS	Brain Anterior Caudate	brain
29	chr19:52074000-52075000	Active TSS	Brain Cingulate Gyrus	brain
30	chr19:52074000-52075000	Active TSS	Brain Hippocampus Middle	brain
31	chr19:52074000-52075000	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr19:52074000-52075000	Active TSS	Fetal Brain Female	brain
33	chr19:52074000-52075000	Active TSS	Hela-S3	cervix
34	chr19:52074000-52075000	Active TSS	HMEC	breast
35	chr19:52074000-52075000	Active TSS	NHLF	lung
36	chr19:52074000-52075200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:52074000-52075200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:52074000-52075200	Active TSS	Muscle Satellite Cultured Cells	--
39	chr19:52074000-52075200	Active TSS	Brain Germinal Matrix	brain
40	chr19:52074000-52075200	Active TSS	NHDF-Ad	bronchial
41	chr19:52074000-52075400	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr19:52074000-52075400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:52074000-52075600	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr19:52074000-52075600	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr19:52074000-52075800	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr19:52074000-52075800	Active TSS	K562	blood
47	chr19:52074000-52076000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr19:52074200-52074400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr19:52074200-52074400	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr19:52074200-52074400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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