Variant report

Variant	rs62114984
Chromosome Location	chr19:52097660-52097661
allele	C/G
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	GABPA	chr19:52097487-52097993	SK-N-SH	brain:	n/a	chr19:52097639-52097648 chr19:52097639-52097653 chr19:52097639-52097650 chr19:52097636-52097650
2	MXI1	chr19:52097557-52097922	HepG2	liver:	n/a	n/a
3	MAX	chr19:52097011-52098187	A549	lung:	n/a	n/a
4	RELA	chr19:52097515-52098061	GM19099	blood:	n/a	n/a
5	MAX	chr19:52097398-52097906	Hela-S3	cervix:	n/a	n/a
6	MAFK	chr19:52097461-52097867	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr19:52097152-52097907	H1-hESC	embryonic stem cell:	n/a	n/a
8	FOXP2	chr19:52097495-52097976	SK-N-MC	brain:	n/a	n/a
9	CBX3	chr19:52097436-52098009	K562	blood:	n/a	n/a
10	CHD2	chr19:52097212-52097989	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr19:52097605-52098206	MCF-7	breast:	n/a	n/a
12	POLR2A	chr19:52097371-52098150	GM12892	blood:	n/a	n/a
13	ELF1	chr19:52097529-52098067	SK-N-SH	brain:	n/a	chr19:52097710-52097719
14	JUND	chr19:52097486-52098105	K562	blood:	n/a	n/a
15	ELF1	chr19:52097487-52098091	MCF-7	breast:	n/a	chr19:52097710-52097719
16	POLR2A	chr19:52097213-52098016	GM15510	blood:	n/a	n/a
17	GABPA	chr19:52097594-52097931	GM12878	blood:	n/a	chr19:52097639-52097648 chr19:52097639-52097653 chr19:52097639-52097650 chr19:52097636-52097650
18	YY1	chr19:52097498-52098179	A549	lung:	n/a	chr19:52098008-52098016 chr19:52097707-52097718
19	SP1	chr19:52097432-52097984	GM12878	blood:	n/a	n/a
20	TBL1XR1	chr19:52097537-52097900	K562	blood:	n/a	n/a
21	PAX5	chr19:52097566-52097933	GM12892	blood:	n/a	n/a
22	SIX5	chr19:52097484-52097965	K562	blood:	n/a	chr19:52097796-52097805 chr19:52097729-52097738 chr19:52097829-52097838
23	ZNF143	chr19:52097506-52098053	Hela-S3	cervix:	n/a	chr19:52097822-52097840 chr19:52097729-52097738 chr19:52097722-52097740 chr19:52097831-52097840 chr19:52097789-52097807 chr19:52097796-52097805 chr19:52097829-52097838
24	YY1	chr19:52097511-52098169	GM12892	blood:	n/a	chr19:52098008-52098016 chr19:52097707-52097718
25	POLR2A	chr19:52096649-52098159	GM12878	blood:	n/a	n/a
26	MAX	chr19:52097471-52097935	K562	blood:	n/a	n/a
27	CREB1	chr19:52097513-52098185	H1-hESC	embryonic stem cell:	n/a	chr19:52097943-52097956
28	POLR2A	chr19:52097124-52098203	MCF-7	breast:	n/a	n/a
29	BCL3	chr19:52097374-52098262	A549	lung:	n/a	chr19:52097706-52097719 chr19:52097907-52097920
30	POLR2A	chr19:52097317-52097810	ECC-1	luminal epithelium:	n/a	n/a
31	BRCA1	chr19:52097528-52097988	Hela-S3	cervix:	n/a	n/a
32	ZMIZ1	chr19:52097416-52097992	K562	blood:	n/a	n/a
33	JUND	chr19:52097606-52098103	H1-hESC	embryonic stem cell:	n/a	n/a
34	YY1	chr19:52097363-52098111	ECC-1	luminal epithelium:	n/a	chr19:52098008-52098016 chr19:52097707-52097718
35	SIX5	chr19:52097479-52098022	K562	blood:	n/a	chr19:52097796-52097805 chr19:52097729-52097738 chr19:52097829-52097838
36	GABPA	chr19:52097608-52097914	K562	blood:	n/a	chr19:52097639-52097648 chr19:52097639-52097653 chr19:52097639-52097650 chr19:52097636-52097650
37	NRF1	chr19:52096917-52098423	SK-N-SH	brain:	n/a	chr19:52097639-52097648 chr19:52097639-52097653 chr19:52097639-52097650 chr19:52097636-52097650 chr19:52097644-52097655
38	HCFC1	chr19:52097053-52098362	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr19:52095177-52098004	U87	brain:	n/a	n/a
40	POLR2A	chr19:52097352-52097933	U87	brain:	n/a	n/a
41	POLR2A	chr19:52097466-52097674	Hela-S3	cervix:	n/a	n/a
42	MAX	chr19:52097491-52098197	A549	lung:	n/a	n/a
43	NRF1	chr19:52097555-52097812	HepG2	liver:	n/a	chr19:52097639-52097648 chr19:52097639-52097653 chr19:52097639-52097650 chr19:52097636-52097650 chr19:52097644-52097655
44	SETDB1	chr19:52097506-52098248	K562	blood:	n/a	chr19:52097640-52097649 chr19:52097718-52097742 chr19:52097818-52097842
45	PML	chr19:52097214-52098091	GM12878	blood:	n/a	n/a
46	ATF3	chr19:52097523-52097947	K562	blood:	n/a	n/a
47	POLR2A	chr19:52097285-52097857	PFSK-1	brain:	n/a	n/a
48	E2F6	chr19:52097576-52097774	K562	blood:	n/a	chr19:52097640-52097649
49	TBP	chr19:52097633-52098102	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr19:52097515-52097961	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:52097626-52097676	NHDF-neo	bronchial:	n/a
2	chr19:52097626-52097676	NB4	blood:	n/a
3	chr19:52097626-52097676	BE2_C	brain:	n/a
4	chr19:52097626-52097676	PANC-1	pancreas:	n/a
5	chr19:52097626-52097676	AG09319	gingival:	n/a
6	chr19:52097626-52097676	K562	blood:	n/a
7	chr19:52097626-52097676	HRPEpiC	eye:	n/a
8	chr19:52097626-52097676	HPAEpiC	pulmonary alveolar:	n/a
9	chr19:52097626-52097676	IMR90	lung:	fetal
10	chr19:52097626-52097676	GM12891	blood:	n/a
11	chr19:52097626-52097676	HCM	heart:	n/a
12	chr19:52097626-52097676	HIPEpiC	eye:	n/a
13	chr19:52097626-52097676	HepG2	liver:	n/a
14	chr19:52097626-52097676	AG10803	skin:	n/a
15	chr19:52097626-52097676	A549	lung:	n/a
16	chr19:52097626-52097676	BJ	skin:	n/a
17	chr19:52097626-52097676	HNPCEpiC	eye:	n/a
18	chr19:52097626-52097676	HCF	heart:	n/a
19	chr19:52097626-52097676	SK-N-SH_RA	brain:	n/a
20	chr19:52097626-52097676	GM19239	blood:	n/a
21	chr19:52097626-52097676	CMK	blood:	n/a
22	chr19:52097626-52097676	Caco-2	colon:	n/a
23	chr19:52097626-52097676	ECC-1	luminal epithelium:	n/a
24	chr19:52097626-52097676	SAEC	small airway:	n/a
25	chr19:52097626-52097676	H1-hESC	embryonic stem cell:	embryo
26	chr19:52097626-52097676	HMEC	breast:	n/a
27	chr19:52097626-52097676	U87	brain:	n/a
28	chr19:52097626-52097676	AG04450	lung:	fetal
29	chr19:52097626-52097676	AoSMC	blood vessel:	n/a
30	chr19:52097626-52097676	HUVEC	blood vessel:	n/a
31	chr19:52097626-52097676	GM12878	blood:	n/a
32	chr19:52097626-52097676	SK-N-MC	brain:	n/a
33	chr19:52097626-52097676	SK-N-SH	brain:	n/a
34	chr19:52097626-52097676	AG04449	skin:	fetal
35	chr19:52097626-52097676	GM12892	blood:	n/a
36	chr19:52097626-52097676	MCF-7	breast:	n/a
37	chr19:52097626-52097676	HEK293	kidney:	embryo
38	chr19:52097626-52097676	Jurkat	blood:	n/a
39	chr19:52097626-52097676	GM06990	blood:	n/a
40	chr19:52097626-52097676	HAEpiC	amniotic membrane:	n/a
41	chr19:52097626-52097676	HL-60	blood:	n/a
42	chr19:52097626-52097676	MCF10A-Er-Src	breast:	n/a
43	chr19:52097626-52097676	ovcar-3	ovarian:	n/a
44	chr19:52097626-52097676	NH-A	brain:	n/a
45	chr19:52097626-52097676	PrEC	prostate:	n/a
46	chr19:52097626-52097676	HRE	kidney:	n/a
47	chr19:52097626-52097676	HCT-116	colon:	n/a
48	chr19:52097626-52097676	Hela-S3	cervix:	n/a
49	chr19:52097626-52097676	LNCaP	prostate:	n/a
50	chr19:52097626-52097676	AG09309	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52095454..52097791-chr19:52104410..52105932,2	K562	blood:
2	chr19:51869850..51871538-chr19:52096656..52099033,2	K562	blood:
3	chr19:52096005..52097791-chr19:52103717..52105932,2	K562	blood:
4	chr19:51897297..51899400-chr19:52095029..52099296,3	K562	blood:
5	chr19:52073066..52077206-chr19:52096074..52099799,4	K562	blood:

Variant related genes	Relation type
ENSG00000167765	TF binding region
ENSG00000269388	TF binding region
ENSG00000267808	TF binding region
ENSG00000269388	CpG island
ENSG00000267808	CpG island
ENSG00000167765	CpG island
ENSG00000160318	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000105497	Chromatin interaction
ENSG00000268889	Chromatin interaction
ENSG00000269403	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11084092	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3794982	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3794983	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794984	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4801881	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4802822	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7252645	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7252767	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs883979	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases
10	nsv9740	chr19:52096231-52107021	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52096600-52098000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:52096600-52098200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr19:52096600-52098200	Active TSS	Muscle Satellite Cultured Cells	--
4	chr19:52096600-52098200	Active TSS	Fetal Kidney	kidney
5	chr19:52096600-52098400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:52096600-52098400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:52096600-52098400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr19:52096600-52098400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr19:52096600-52098400	Active TSS	NHDF-Ad	bronchial
10	chr19:52096600-52098600	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr19:52096600-52098600	Active TSS	A549	lung
12	chr19:52096600-52098800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:52096800-52098000	Active TSS	H1 Cell Line	embryonic stem cell
14	chr19:52096800-52098000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:52096800-52098000	Active TSS	HMEC	breast
16	chr19:52096800-52098200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr19:52096800-52098200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr19:52096800-52098200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr19:52096800-52098400	Active TSS	H9 Cell Line	embryonic stem cell
20	chr19:52096800-52098400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr19:52096800-52098400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:52096800-52098400	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr19:52096800-52098400	Active TSS	Fetal Intestine Large	intestine
24	chr19:52096800-52098400	Active TSS	Rectal Smooth Muscle	rectum
25	chr19:52096800-52098400	Active TSS	HSMMtube	muscle
26	chr19:52096800-52098600	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr19:52097000-52098000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:52097000-52098200	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr19:52097000-52098200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:52097000-52098200	Active TSS	Aorta	Aorta
31	chr19:52097000-52098200	Active TSS	Right Ventricle	heart
32	chr19:52097000-52098200	Flanking Active TSS	HUVEC	blood vessel
33	chr19:52097000-52098400	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr19:52097000-52098400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr19:52097000-52098400	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr19:52097000-52098400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr19:52097000-52098400	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr19:52097000-52098400	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr19:52097000-52098400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr19:52097000-52098400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:52097000-52098400	Active TSS	Gastric	stomach
42	chr19:52097000-52098400	Active TSS	Psoas Muscle	Psoas
43	chr19:52097000-52098600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr19:52097000-52098600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr19:52097200-52097800	Active TSS	Fetal Thymus	thymus
46	chr19:52097200-52098000	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr19:52097200-52098000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:52097200-52098000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:52097200-52098000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:52097200-52098000	Active TSS	Brain Cingulate Gyrus	brain

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