Variant report

Variant	rs7257275
Chromosome Location	chr19:51893931-51893932
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:56)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:56 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:51893517-51894127	K562	blood:	n/a	n/a
2	ELF1	chr19:51893625-51894700	K562	blood:	n/a	chr19:51894151-51894164
3	POLR2A	chr19:51893452-51894272	H1-hESC	embryonic stem cell:	n/a	n/a
4	IRF1	chr19:51893820-51894914	K562	blood:	n/a	chr19:51893857-51893871 chr19:51893884-51893898
5	HMGN3	chr19:51893755-51893997	K562	blood:	n/a	n/a
6	REST	chr19:51893654-51894009	K562	blood:	n/a	n/a
7	SP4	chr19:51893694-51894054	H1-hESC	embryonic stem cell:	n/a	chr19:51893882-51893898 chr19:51893855-51893871 chr19:51893836-51893847
8	HEY1	chr19:51893787-51894273	K562	blood:	n/a	n/a
9	TAF1	chr19:51893628-51894437	K562	blood:	n/a	n/a
10	EP300	chr19:51893647-51894676	K562	blood:	n/a	n/a
11	TBL1XR1	chr19:51893569-51894133	K562	blood:	n/a	n/a
12	POLR2A	chr19:51893611-51894582	K562	blood:	n/a	n/a
13	TAF1	chr19:51893587-51894111	K562	blood:	n/a	n/a
14	ZBTB7A	chr19:51893628-51894642	K562	blood:	n/a	chr19:51893821-51893829
15	GABPA	chr19:51893922-51894533	K562	blood:	n/a	n/a
16	POLR2A	chr19:51893574-51894505	K562	blood:	n/a	n/a
17	IRF1	chr19:51893672-51894536	K562	blood:	n/a	chr19:51893857-51893871 chr19:51893884-51893898
18	ZBTB7A	chr19:51893583-51894672	K562	blood:	n/a	chr19:51893821-51893829
19	ZMIZ1	chr19:51893755-51894186	K562	blood:	n/a	n/a
20	PML	chr19:51893491-51894381	K562	blood:	n/a	n/a
21	TBP	chr19:51893700-51894391	K562	blood:	n/a	n/a
22	CCNT2	chr19:51893787-51893987	K562	blood:	n/a	n/a
23	POLR2A	chr19:51893569-51894644	K562	blood:	n/a	n/a
24	POLR2A	chr19:51893711-51894680	K562	blood:	n/a	n/a
25	HEY1	chr19:51893572-51894687	K562	blood:	n/a	n/a
26	JUN	chr19:51893798-51894318	K562	blood:	n/a	n/a
27	CHD2	chr19:51893693-51894283	H1-hESC	embryonic stem cell:	n/a	n/a
28	TEAD4	chr19:51893556-51894601	K562	blood:	n/a	n/a
29	GTF2B	chr19:51893797-51894103	K562	blood:	n/a	n/a
30	CHD2	chr19:51893764-51894238	K562	blood:	n/a	n/a
31	POLR2A	chr19:51893555-51894092	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr19:51893610-51894575	K562	blood:	n/a	n/a
33	MYC	chr19:51893614-51894027	K562	blood:	n/a	n/a
34	POLR2A	chr19:51893476-51894707	K562	blood:	n/a	n/a
35	TBP	chr19:51893591-51893939	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr19:51893602-51894691	K562	blood:	n/a	n/a
37	ELF1	chr19:51893620-51894580	GM12878	blood:	n/a	chr19:51894151-51894164
38	ELF1	chr19:51893925-51894563	GM12878	blood:	n/a	chr19:51894151-51894164
39	SP1	chr19:51893588-51894029	H1-hESC	embryonic stem cell:	n/a	chr19:51893885-51893895 chr19:51893857-51893869 chr19:51893838-51893847 chr19:51893854-51893868 chr19:51893836-51893847 chr19:51893885-51893895 chr19:51893859-51893868
40	TBL1XR1	chr19:51893629-51894092	K562	blood:	n/a	n/a
41	GTF2F1	chr19:51893771-51893939	H1-hESC	embryonic stem cell:	n/a	n/a
42	RCOR1	chr19:51893664-51894795	K562	blood:	n/a	n/a
43	JUND	chr19:51893603-51894064	K562	blood:	n/a	n/a
44	NR2F2	chr19:51893568-51894732	K562	blood:	n/a	n/a
45	ZNF263	chr19:51893829-51894442	K562	blood:	n/a	n/a
46	ZNF143	chr19:51893847-51893990	H1-hESC	embryonic stem cell:	n/a	n/a
47	ZNF143	chr19:51893801-51894047	K562	blood:	n/a	n/a
48	ELF1	chr19:51893674-51894655	K562	blood:	n/a	chr19:51894151-51894164
49	CBX3	chr19:51893588-51893982	K562	blood:	n/a	n/a
50	TAF1	chr19:51893477-51894163	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:51893899-51893949	HCPEpiC	choroid plexus:	n/a
2	chr19:51893899-51893949	SKMC	muscle:	n/a
3	chr19:51893899-51893949	SK-N-SH	brain:	n/a
4	chr19:51893899-51893949	PANC-1	pancreas:	n/a
5	chr19:51893899-51893949	NH-A	brain:	n/a
6	chr19:51893899-51893949	HCF	heart:	n/a
7	chr19:51893899-51893949	SK-N-MC	brain:	n/a
8	chr19:51893899-51893949	RPTEC	kidney:	n/a
9	chr19:51893899-51893949	CMK	blood:	n/a
10	chr19:51893899-51893949	T-47D	breast:	n/a
11	chr19:51893899-51893949	HIPEpiC	eye:	n/a
12	chr19:51893899-51893949	MCF10A-Er-Src	breast:	n/a
13	chr19:51893899-51893949	Hela-S3	cervix:	n/a
14	chr19:51893899-51893949	PFSK-1	brain:	n/a
15	chr19:51893899-51893949	HepG2	liver:	n/a
16	chr19:51893899-51893949	HRCEpiC	kidney:	n/a
17	chr19:51893899-51893949	GM06990	blood:	n/a
18	chr19:51893899-51893949	BE2_C	brain:	n/a
19	chr19:51893899-51893949	A549	lung:	n/a
20	chr19:51893899-51893949	GM12891	blood:	n/a
21	chr19:51893899-51893949	PrEC	prostate:	n/a
22	chr19:51893899-51893949	HRPEpiC	eye:	n/a
23	chr19:51893899-51893949	BJ	skin:	n/a
24	chr19:51893899-51893949	MCF-7	breast:	n/a
25	chr19:51893899-51893949	HNPCEpiC	eye:	n/a
26	chr19:51893899-51893949	HAEpiC	amniotic membrane:	n/a
27	chr19:51893899-51893949	HUVEC	blood vessel:	n/a
28	chr19:51893899-51893949	NT2-D1	testis:	n/a
29	chr19:51893899-51893949	HEEpiC	esophagus:	n/a
30	chr19:51893899-51893949	HPAEpiC	pulmonary alveolar:	n/a
31	chr19:51893899-51893949	Jurkat	blood:	n/a
32	chr19:51893899-51893949	GM12892	blood:	n/a
33	chr19:51893899-51893949	HEK293	kidney:	embryo
34	chr19:51893899-51893949	LNCaP	prostate:	n/a
35	chr19:51893899-51893949	IMR90	lung:	fetal
36	chr19:51893899-51893949	K562	blood:	n/a
37	chr19:51893899-51893949	NHBE	bronchial:	n/a
38	chr19:51893899-51893949	ovcar-3	ovarian:	n/a
39	chr19:51893899-51893949	H1-hESC	embryonic stem cell:	embryo
40	chr19:51893899-51893949	NB4	blood:	n/a
41	chr19:51893899-51893949	AG04449	skin:	fetal
42	chr19:51893899-51893949	AG10803	skin:	n/a
43	chr19:51893899-51893949	HRE	kidney:	n/a
44	chr19:51893899-51893949	NHDF-neo	bronchial:	n/a
45	chr19:51893899-51893949	SAEC	small airway:	n/a
46	chr19:51893899-51893949	Hepatocyte	liver:	n/a
47	chr19:51893899-51893949	U87	brain:	n/a
48	chr19:51893899-51893949	ECC-1	luminal epithelium:	n/a
49	chr19:51893899-51893949	SK-N-SH_RA	brain:	n/a
50	chr19:51893899-51893949	AG09309	skin:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51841717..51843747-chr19:51891710..51894546,2	K562	blood:
2	chr19:51840838..51845657-chr19:51892354..51900411,18	K562	blood:
3	chr19:51889722..51893942-chr19:51894149..51900029,8	K562	blood:
4	chr19:51867772..51875803-chr19:51892381..51899756,21	K562	blood:
5	chr19:51889349..51894566-chr19:51895156..51899826,6	K562	blood:
6	chr19:51864453..51872845-chr19:51892428..51902096,29	K562	blood:

No data

Variant related genes	Relation type
LIM2	TF binding region
ENSG00000268889	TF binding region
C19orf84	TF binding region
LIM2	CpG island
ENSG00000268889	CpG island
C19orf84	CpG island
ENSG00000105379	Chromatin interaction
ENSG00000186806	Chromatin interaction
ENSG00000269403	Chromatin interaction
ENSG00000267905	Chromatin interaction
ENSG00000160318	Chromatin interaction
ENSG00000105374	Chromatin interaction
ENSG00000268520	Chromatin interaction
ENSG00000268889	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10403762	0.81[ASN][1000 genomes]
rs10404198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10419880	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11084075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11669975	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11670065	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11673263	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2411321	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2411322	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2547308	0.96[ASN][1000 genomes]
rs2547309	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2741240	0.92[ASN][1000 genomes]
rs2741241	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3810093	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810094	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3810095	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3810096	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3810097	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826657	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826658	0.97[ASN][1000 genomes]
rs3826659	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3826660	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826662	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3826663	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826664	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826665	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4377257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4441376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250926	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7251238	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7251286	0.82[EUR][1000 genomes]
rs7251311	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7251566	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7508570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100861	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8104425	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107533	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7257275	CTD-2616J11.4	cis	Whole Blood	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51872000-51897000	Weak transcription	Right Atrium	heart
2	chr19:51889200-51897000	Weak transcription	Spleen	Spleen
3	chr19:51891000-51894400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr19:51891000-51897000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr19:51891200-51894200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:51891600-51897000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:51891800-51894000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:51891800-51897000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:51891800-51897000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:51891800-51897000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:51892400-51894200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:51892400-51894200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr19:51892600-51894800	Active TSS	Fetal Intestine Small	intestine
14	chr19:51892600-51897000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:51893000-51894800	Enhancers	HepG2	liver
16	chr19:51893400-51894200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr19:51893400-51894400	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr19:51893400-51894400	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr19:51893600-51894000	Enhancers	Primary B cells from cord blood	blood
20	chr19:51893600-51894000	Enhancers	Primary hematopoietic stem cells	blood
21	chr19:51893600-51894000	Active TSS	Fetal Intestine Large	intestine
22	chr19:51893600-51894000	Enhancers	Fetal Lung	lung
23	chr19:51893600-51894000	Enhancers	Fetal Muscle Trunk	muscle
24	chr19:51893600-51894000	Enhancers	Thymus	Thymus
25	chr19:51893600-51894200	Enhancers	H1 Cell Line	embryonic stem cell
26	chr19:51893600-51894200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr19:51893600-51894200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:51893600-51894200	Enhancers	Placenta	Placenta
29	chr19:51893600-51894200	Enhancers	Fetal Stomach	stomach
30	chr19:51893600-51894400	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr19:51893600-51894400	Enhancers	Fetal Muscle Leg	muscle
32	chr19:51893600-51894400	Flanking Active TSS	Fetal Thymus	thymus
33	chr19:51893600-51894600	Active TSS	H9 Cell Line	embryonic stem cell
34	chr19:51893600-51894600	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr19:51893600-51894600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr19:51893600-51894600	Enhancers	Primary B cells from peripheral blood	blood
37	chr19:51893600-51894600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr19:51893600-51894800	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr19:51893600-51894800	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr19:51893600-51894800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:51893600-51894800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:51893800-51894000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr19:51893800-51894000	Enhancers	GM12878-XiMat	blood
44	chr19:51893800-51894000	Enhancers	K562	blood
45	chr19:51893800-51894200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr19:51893800-51894400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr19:51893800-51894400	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr19:51893800-51894600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:51893800-51894800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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