Variant report

Variant	rs7258385
Chromosome Location	chr19:38183232-38183233
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:186)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:186 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr19:38183090-38183458	K562	blood:	n/a	n/a
2	POLR2A	chr19:38183133-38183385	MCF-7	breast:	n/a	n/a
3	YY1	chr19:38182815-38183456	SK-N-SH_RA	brain:	n/a	n/a
4	MAX	chr19:38183104-38183437	K562	blood:	n/a	n/a
5	TAF1	chr19:38182919-38183435	HepG2	liver:	n/a	n/a
6	HCFC1	chr19:38183029-38183419	K562	blood:	n/a	n/a
7	CTCF	chr19:38183025-38183390	Spleen_OC	spleen:	n/a	n/a
8	POLR2A	chr19:38182932-38183552	NB4	blood:	n/a	n/a
9	CREB1	chr19:38182955-38183423	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:38183009-38183443	MCF-7	breast:	n/a	n/a
11	MAZ	chr19:38183014-38183389	K562	blood:	n/a	n/a
12	TAF1	chr19:38182770-38183412	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:38182651-38183662	PFSK-1	brain:	n/a	n/a
14	MAX	chr19:38182654-38183579	HepG2	liver:	n/a	n/a
15	CTCF	chr19:38183029-38183262	GM12891	blood:	n/a	n/a
16	ZNF143	chr19:38183043-38183441	K562	blood:	n/a	chr19:38183234-38183243 chr19:38183125-38183135 chr19:38183236-38183255
17	TAF1	chr19:38183096-38183475	H1-neurons	neurons:	n/a	n/a
18	CTCF	chr19:38183100-38183250	GM12873	blood:	n/a	n/a
19	RCOR1	chr19:38183041-38183378	K562	blood:	n/a	n/a
20	CTCF	chr19:38183140-38183290	GM12871	blood:	n/a	n/a
21	CREB1	chr19:38182825-38183465	H1-hESC	embryonic stem cell:	n/a	n/a
22	MYC	chr19:38183220-38183238	K562	blood:	n/a	n/a
23	CTCF	chr19:38183120-38183270	HepG2	liver:	n/a	n/a
24	CTCF	chr19:38183034-38183265	Medullo	brain:	n/a	n/a
25	BHLHE40	chr19:38183071-38183431	K562	blood:	n/a	n/a
26	POLR2A	chr19:38182963-38183448	HUVEC	blood vessel:	n/a	n/a
27	CHD2	chr19:38183183-38183351	K562	blood:	n/a	n/a
28	E2F6	chr19:38183054-38183479	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr19:38183066-38183463	GM12878	blood:	n/a	n/a
30	NFIC	chr19:38182787-38183298	HepG2	liver:	n/a	n/a
31	CTCF	chr19:38183100-38183250	AG10803	skin:	n/a	n/a
32	UBTF	chr19:38182782-38183419	K562	blood:	n/a	n/a
33	CTBP2	chr19:38182811-38183463	H1-hESC	embryonic stem cell:	n/a	n/a
34	CREB1	chr19:38182730-38183502	HepG2	liver:	n/a	n/a
35	MAX	chr19:38182877-38183425	HepG2	liver:	n/a	n/a
36	E2F6	chr19:38183201-38183405	K562	blood:	n/a	n/a
37	CREB1	chr19:38182851-38183470	K562	blood:	n/a	n/a
38	CTCF	chr19:38183140-38183290	SAEC	small airway:	n/a	n/a
39	POLR2A	chr19:38183011-38183616	K562	blood:	n/a	n/a
40	SIX5	chr19:38183120-38183285	K562	blood:	n/a	chr19:38183234-38183243
41	JUND	chr19:38183006-38183325	HepG2	liver:	n/a	chr19:38183047-38183055
42	CTCF	chr19:38183140-38183290	BJ	skin:	n/a	n/a
43	SIN3A	chr19:38182817-38183437	H1-hESC	embryonic stem cell:	n/a	n/a
44	ZNF143	chr19:38182994-38183472	H1-hESC	embryonic stem cell:	n/a	chr19:38183234-38183243 chr19:38183125-38183135 chr19:38183236-38183255
45	GTF2F1	chr19:38183085-38183317	K562	blood:	n/a	n/a
46	POLR2A	chr19:38182767-38183546	HepG2	liver:	n/a	n/a
47	POLR2A	chr19:38182798-38183559	HepG2	liver:	n/a	n/a
48	CTCF	chr19:38183141-38183249	GM12878	blood:	n/a	n/a
49	CREB1	chr19:38182827-38183470	H1-hESC	embryonic stem cell:	n/a	n/a
50	ARID3A	chr19:38182858-38183497	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:38183210-38183260	NHBE	bronchial:	n/a
2	chr19:38183210-38183260	ECC-1	luminal epithelium:	n/a
3	chr19:38183210-38183260	LNCaP	prostate:	n/a
4	chr19:38183210-38183260	HCF	heart:	n/a
5	chr19:38183210-38183260	NH-A	brain:	n/a
6	chr19:38183210-38183260	HCM	heart:	n/a
7	chr19:38183210-38183260	MCF-7	breast:	n/a
8	chr19:38183210-38183260	GM06990	blood:	n/a
9	chr19:38183210-38183260	SK-N-SH	brain:	n/a
10	chr19:38183210-38183260	BJ	skin:	n/a
11	chr19:38183210-38183260	NT2-D1	testis:	n/a
12	chr19:38183210-38183260	RPTEC	kidney:	n/a
13	chr19:38183210-38183260	HCT-116	colon:	n/a
14	chr19:38183210-38183260	GM12892	blood:	n/a
15	chr19:38183210-38183260	AG09309	skin:	n/a
16	chr19:38183210-38183260	HIPEpiC	eye:	n/a
17	chr19:38183210-38183260	SK-N-SH_RA	brain:	n/a
18	chr19:38183210-38183260	AG04449	skin:	fetal
19	chr19:38183210-38183260	PFSK-1	brain:	n/a
20	chr19:38183210-38183260	CMK	blood:	n/a
21	chr19:38183210-38183260	HMEC	breast:	n/a
22	chr19:38183210-38183260	BE2_C	brain:	n/a
23	chr19:38183210-38183260	GM19239	blood:	n/a
24	chr19:38183210-38183260	AoSMC	blood vessel:	n/a
25	chr19:38183210-38183260	GM12891	blood:	n/a
26	chr19:38183210-38183260	Hela-S3	cervix:	n/a
27	chr19:38183210-38183260	NB4	blood:	n/a
28	chr19:38183210-38183260	PANC-1	pancreas:	n/a
29	chr19:38183210-38183260	HAEpiC	amniotic membrane:	n/a
30	chr19:38183210-38183260	SKMC	muscle:	n/a
31	chr19:38183210-38183260	T-47D	breast:	n/a
32	chr19:38183210-38183260	HepG2	liver:	n/a
33	chr19:38183210-38183260	HL-60	blood:	n/a
34	chr19:38183210-38183260	HRE	kidney:	n/a
35	chr19:38183210-38183260	HEEpiC	esophagus:	n/a
36	chr19:38183210-38183260	IMR90	lung:	fetal
37	chr19:38183210-38183260	U87	brain:	n/a
38	chr19:38183210-38183260	HRCEpiC	kidney:	n/a
39	chr19:38183210-38183260	NHDF-neo	bronchial:	n/a
40	chr19:38183210-38183260	H1-hESC	embryonic stem cell:	embryo
41	chr19:38183210-38183260	AG04450	lung:	fetal
42	chr19:38183210-38183260	HPAEpiC	pulmonary alveolar:	n/a
43	chr19:38183210-38183260	PrEC	prostate:	n/a
44	chr19:38183210-38183260	HUVEC	blood vessel:	n/a
45	chr19:38183210-38183260	GM12878	blood:	n/a
46	chr19:38183210-38183260	HNPCEpiC	eye:	n/a
47	chr19:38183210-38183260	HEK293	kidney:	embryo
48	chr19:38183210-38183260	K562	blood:	n/a
49	chr19:38183210-38183260	AG09319	gingival:	n/a
50	chr19:38183210-38183260	MCF10A-Er-Src	breast:	n/a

No data

Variant related genes	Relation type
ZNF781	TF binding region
ZFP30	TF binding region
ZFP30	CpG island
ZNF781	CpG island

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1060522	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10853710	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11083429	0.81[EUR][1000 genomes]
rs11083433	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11666172	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11668796	0.98[EUR][1000 genomes]
rs11671953	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11673497	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16975299	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17246792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28431170	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2891657	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34991303	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55871826	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55913702	0.98[EUR][1000 genomes]
rs55950325	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62108305	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62108351	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6508739	0.98[EUR][1000 genomes]
rs7249622	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7253081	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73037060	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8102818	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7258385	ZNF573	cis	multi-tissue	Pritchard
rs7258385	AC012309.5	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38181200-38183600	Active TSS	Brain Germinal Matrix	brain
2	chr19:38182000-38183600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr19:38182200-38183400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr19:38182200-38183600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:38182200-38183600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:38182200-38183600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:38182200-38183600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:38182200-38183600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
9	chr19:38182200-38183600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:38182200-38183600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:38182200-38183600	Active TSS	Colon Smooth Muscle	Colon
12	chr19:38182200-38183600	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr19:38182200-38183600	Active TSS	Fetal Kidney	kidney
14	chr19:38182200-38183600	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr19:38182200-38183600	Active TSS	Psoas Muscle	Psoas
16	chr19:38182200-38183600	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr19:38182200-38183600	Active TSS	Stomach Smooth Muscle	stomach
18	chr19:38182200-38183600	Active TSS	HepG2	liver
19	chr19:38182200-38183600	Active TSS	NHDF-Ad	bronchial
20	chr19:38182200-38183600	Active TSS	NHLF	lung
21	chr19:38182200-38183600	Active TSS	Osteobl	bone
22	chr19:38182200-38184000	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr19:38182200-38184200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:38182200-38184200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:38182200-38184200	Active TSS	Duodenum Mucosa	Duodenum
26	chr19:38182200-38184200	Flanking Active TSS	Dnd41	blood
27	chr19:38182200-38184400	Active TSS	Brain Hippocampus Middle	brain
28	chr19:38182400-38183600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:38182400-38183600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr19:38182400-38183600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
31	chr19:38182400-38183600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:38182400-38183600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
33	chr19:38182400-38183600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr19:38182400-38183600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr19:38182400-38183600	Active TSS	Muscle Satellite Cultured Cells	--
36	chr19:38182400-38183600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:38182400-38183600	Active TSS	Aorta	Aorta
38	chr19:38182400-38183600	Active TSS	Fetal Intestine Small	intestine
39	chr19:38182400-38183600	Active TSS	Fetal Muscle Leg	muscle
40	chr19:38182400-38183600	Active TSS	Fetal Stomach	stomach
41	chr19:38182400-38183600	Active TSS	Ovary	ovary
42	chr19:38182400-38183600	Active TSS	Rectal Smooth Muscle	rectum
43	chr19:38182400-38183600	ZNF genes & repeats	GM12878-XiMat	blood
44	chr19:38182400-38183600	Active TSS	NH-A	brain
45	chr19:38182400-38183800	Active TSS	Fetal Muscle Trunk	muscle
46	chr19:38182400-38184000	Active TSS	Fetal Lung	lung
47	chr19:38182400-38184200	Active TSS	Brain Angular Gyrus	brain
48	chr19:38182400-38184200	Active TSS	Fetal Brain Male	brain
49	chr19:38182400-38184400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:38182600-38183400	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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