Variant report

Variant	rs426076
Chromosome Location	chr19:39572050-39572051
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39571872-39572335	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:39572000-39572050	HepG2	liver:	n/a
2	chr19:39572000-39572050	AoSMC	blood vessel:	n/a
3	chr19:39572000-39572050	HUVEC	blood vessel:	n/a
4	chr19:39572000-39572050	HEEpiC	esophagus:	n/a
5	chr19:39572000-39572050	SK-N-SH_RA	brain:	n/a
6	chr19:39572000-39572050	BE2_C	brain:	n/a
7	chr19:39572000-39572050	HAEpiC	amniotic membrane:	n/a
8	chr19:39572000-39572050	GM12891	blood:	n/a
9	chr19:39572000-39572050	AG04450	lung:	fetal
10	chr19:39572000-39572050	HCF	heart:	n/a
11	chr19:39572000-39572050	ovcar-3	ovarian:	n/a
12	chr19:39572000-39572050	NT2-D1	testis:	n/a
13	chr19:39572000-39572050	HPAEpiC	pulmonary alveolar:	n/a
14	chr19:39572000-39572050	HL-60	blood:	n/a
15	chr19:39572000-39572050	Hepatocyte	liver:	n/a
16	chr19:39572000-39572050	AG09319	gingival:	n/a
17	chr19:39572000-39572050	ProgFib	skin:	n/a
18	chr19:39572000-39572050	HNPCEpiC	eye:	n/a
19	chr19:39572000-39572050	A549	lung:	n/a
20	chr19:39572000-39572050	H1-hESC	embryonic stem cell:	embryo
21	chr19:39572000-39572050	U87	brain:	n/a
22	chr19:39572000-39572050	ECC-1	luminal epithelium:	n/a
23	chr19:39572000-39572050	HRCEpiC	kidney:	n/a
24	chr19:39572000-39572050	HCT-116	colon:	n/a
25	chr19:39572000-39572050	MCF-7	breast:	n/a
26	chr19:39572000-39572050	BJ	skin:	n/a
27	chr19:39572000-39572050	SK-N-SH	brain:	n/a
28	chr19:39572000-39572050	HCPEpiC	choroid plexus:	n/a
29	chr19:39572000-39572050	AG04449	skin:	fetal
30	chr19:39572000-39572050	GM12878	blood:	n/a
31	chr19:39572000-39572050	Caco-2	colon:	n/a
32	chr19:39572000-39572050	IMR90	lung:	fetal
33	chr19:39572000-39572050	RPTEC	kidney:	n/a
34	chr19:39572000-39572050	Hela-S3	cervix:	n/a
35	chr19:39572000-39572050	NHDF-neo	bronchial:	n/a
36	chr19:39572000-39572050	HRPEpiC	eye:	n/a
37	chr19:39572000-39572050	AG10803	skin:	n/a
38	chr19:39572000-39572050	MCF10A-Er-Src	breast:	n/a
39	chr19:39572000-39572050	LNCaP	prostate:	n/a
40	chr19:39572000-39572050	HEK293	kidney:	embryo
41	chr19:39572000-39572050	HRE	kidney:	n/a
42	chr19:39572000-39572050	GM12892	blood:	n/a
43	chr19:39572000-39572050	NB4	blood:	n/a
44	chr19:39572000-39572050	HCM	heart:	n/a
45	chr19:39572000-39572050	SAEC	small airway:	n/a
46	chr19:39572000-39572050	PrEC	prostate:	n/a
47	chr19:39572000-39572050	PFSK-1	brain:	n/a
48	chr19:39572000-39572050	GM06990	blood:	n/a
49	chr19:39572000-39572050	Jurkat	blood:	n/a
50	chr19:39572000-39572050	GM19239	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39522794..39525227-chr19:39570722..39573005,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000183760	TF binding region
ENSG00000183760	CpG island
ENSG00000161243	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10407957	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10408661	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12151180	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2569365	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34738600	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs377373	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs380679	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs384605	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385681	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs392005	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs392135	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs393559	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs395387	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs396616	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs397189	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs400011	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs420682	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs452666	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs453853	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4802015	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803196	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803197	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs482679	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs487456	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs578940	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs597995	0.95[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs602744	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs609327	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs620642	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs621580	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs648192	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs648635	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs665998	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs690812	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691059	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs691114	0.95[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs691256	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691266	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs691391	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs691890	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs692294	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs692343	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs692347	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs774727	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs774927	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs774928	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv522530	chr19:39552150-39573918	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1067028	chr19:39567228-39622846	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1060469	chr19:39567228-39624790	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs426076	PVRL2	cis	parietal	SCAN
rs426076	TGFB1	cis	parietal	SCAN
rs426076	PSG3	cis	parietal	SCAN
rs426076	GIPR	cis	parietal	SCAN
rs426076	KCNN4	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39565400-39573000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr19:39565400-39573200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:39567400-39574000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:39569800-39573400	Weak transcription	Brain Substantia Nigra	brain
5	chr19:39569800-39573400	Weak transcription	Hela-S3	cervix
6	chr19:39569800-39573600	Weak transcription	HUVEC	blood vessel
7	chr19:39569800-39573800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:39569800-39573800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:39570000-39573000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:39570000-39573000	Weak transcription	NHDF-Ad	bronchial
11	chr19:39570000-39573200	Weak transcription	NHEK	skin
12	chr19:39570200-39573200	Weak transcription	Brain Anterior Caudate	brain
13	chr19:39570400-39573600	Weak transcription	Osteobl	bone
14	chr19:39570600-39573200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:39570800-39573000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:39571200-39572200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:39571400-39573400	Weak transcription	A549	lung
18	chr19:39571600-39573000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:39571800-39572800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:39572000-39572200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:39572000-39573000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:39572000-39573000	Weak transcription	HMEC	breast

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