Variant report

Variant	rs883979
Chromosome Location	chr19:52098125-52098126
allele	A/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	MAX	chr19:52097011-52098187	A549	lung:	n/a	n/a
2	POLR2A	chr19:52097605-52098206	MCF-7	breast:	n/a	n/a
3	POLR2A	chr19:52097371-52098150	GM12892	blood:	n/a	n/a
4	YY1	chr19:52097498-52098179	A549	lung:	n/a	chr19:52098008-52098016 chr19:52097707-52097718
5	POLR2A	chr19:52097742-52098167	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr19:52097511-52098169	GM12892	blood:	n/a	chr19:52098008-52098016 chr19:52097707-52097718
7	POLR2A	chr19:52096649-52098159	GM12878	blood:	n/a	n/a
8	CREB1	chr19:52097513-52098185	H1-hESC	embryonic stem cell:	n/a	chr19:52097943-52097956
9	POLR2A	chr19:52097124-52098203	MCF-7	breast:	n/a	n/a
10	BCL3	chr19:52097374-52098262	A549	lung:	n/a	chr19:52097706-52097719 chr19:52097907-52097920
11	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
12	HCFC1	chr19:52097053-52098362	Hela-S3	cervix:	n/a	n/a
13	MAX	chr19:52097491-52098197	A549	lung:	n/a	n/a
14	SETDB1	chr19:52097506-52098248	K562	blood:	n/a	chr19:52097640-52097649 chr19:52097718-52097742 chr19:52097818-52097842
15	ETS1	chr19:52097399-52098135	A549	lung:	n/a	chr19:52097829-52097842 chr19:52097729-52097742 chr19:52097796-52097809
16	ZC3H11A	chr19:52097325-52098160	K562	blood:	n/a	n/a
17	YY1	chr19:52097601-52098189	K562	blood:	n/a	chr19:52098008-52098016 chr19:52097707-52097718
18	POLR2A	chr19:52095947-52098295	K562	blood:	n/a	n/a
19	MAX	chr19:52097217-52098234	K562	blood:	n/a	n/a
20	ZNF263	chr19:52096973-52098574	HEK293-T-REx	kidney:	n/a	n/a
21	CHD2	chr19:52097118-52098214	K562	blood:	n/a	n/a
22	MYC	chr19:52097637-52098151	H1-hESC	embryonic stem cell:	n/a	n/a
23	YY1	chr19:52097302-52098207	SK-N-SH_RA	brain:	n/a	chr19:52098008-52098016 chr19:52097707-52097718
24	CEBPB	chr19:52097601-52098160	K562	blood:	n/a	n/a
25	CTCF	chr19:52098000-52098150	GM12874	blood:	n/a	n/a
26	ZNF143	chr19:52097417-52098249	K562	blood:	n/a	chr19:52097822-52097840 chr19:52097729-52097738 chr19:52097722-52097740 chr19:52097831-52097840 chr19:52097789-52097807 chr19:52097796-52097805 chr19:52097829-52097838
27	CTCF	chr19:52097980-52098130	GM12869	blood:	n/a	n/a
28	MYC	chr19:52097472-52098336	K562	blood:	n/a	n/a
29	ELF1	chr19:52097562-52098159	K562	blood:	n/a	chr19:52097710-52097719
30	ELF1	chr19:52097514-52098153	MCF-7	breast:	n/a	chr19:52097710-52097719
31	STAT5A	chr19:52097297-52098176	GM12878	blood:	n/a	n/a
32	CTCF	chr19:52098100-52098250	GM12873	blood:	n/a	n/a
33	ELF1	chr19:52097205-52098313	GM12878	blood:	n/a	chr19:52097710-52097719
34	TCF12	chr19:52097149-52098234	A549	lung:	n/a	chr19:52097604-52097611 chr19:52097787-52097797
35	YY1	chr19:52097512-52098145	GM12891	blood:	n/a	chr19:52098008-52098016 chr19:52097707-52097718
36	HCFC1	chr19:52097487-52098490	K562	blood:	n/a	n/a
37	MTA3	chr19:52096806-52098235	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:52097028-52098348	H1-neurons	neurons:	n/a	n/a
39	ETS1	chr19:52097213-52098206	A549	lung:	n/a	chr19:52097829-52097842 chr19:52097729-52097742 chr19:52097796-52097809
40	ELF1	chr19:52097272-52098159	GM12878	blood:	n/a	chr19:52097710-52097719
41	MAZ	chr19:52097043-52098242	K562	blood:	n/a	n/a
42	CTCF	chr19:52098100-52098250	HBMEC	blood vessel:	n/a	n/a
43	YY1	chr19:52097321-52098248	SK-N-SH	brain:	n/a	chr19:52098008-52098016 chr19:52097707-52097718
44	ZEB1	chr19:52097569-52098160	GM12878	blood:	n/a	chr19:52097896-52097905 chr19:52097788-52097799 chr19:52097897-52097904
45	STAT1	chr19:52097229-52098267	GM12878	blood:	n/a	n/a
46	SIX5	chr19:52097441-52098228	A549	lung:	n/a	chr19:52097796-52097805 chr19:52097729-52097738 chr19:52097829-52097838
47	TAF1	chr19:52097366-52098181	H1-neurons	neurons:	n/a	n/a
48	YY1	chr19:52097390-52098229	GM12878	blood:	n/a	chr19:52098008-52098016 chr19:52097707-52097718
49	YY1	chr19:52097529-52098265	GM12878	blood:	n/a	chr19:52098008-52098016 chr19:52097707-52097718
50	CTCF	chr19:52098091-52098167	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52097772..52099435-chr19:52099519..52102447,4	K562	blood:
2	chr19:51869850..51871538-chr19:52096656..52099033,2	K562	blood:
3	chr19:52097873..52100049-chr19:52100051..52101814,3	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
ENSG00000269388	TF binding region
ENSG00000167765	TF binding region
ENSG00000267808	TF binding region
ENSG00000160318	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000269403	Chromatin interaction
ENSG00000105497	Chromatin interaction
ENSG00000268889	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11084092	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2864139	0.80[ASN][1000 genomes]
rs3794982	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794983	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794984	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4801881	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4802822	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62114984	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7252645	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7252767	0.99[EUR][1000 genomes];0.88[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	chr19:52096600-52098200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr19:52096600-52098200	Active TSS	Muscle Satellite Cultured Cells	--
3	chr19:52096600-52098200	Active TSS	Fetal Kidney	kidney
4	chr19:52096600-52098400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:52096600-52098400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr19:52096600-52098400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr19:52096600-52098400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr19:52096600-52098400	Active TSS	NHDF-Ad	bronchial
9	chr19:52096600-52098600	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr19:52096600-52098600	Active TSS	A549	lung
11	chr19:52096600-52098800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:52096800-52098200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr19:52096800-52098200	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr19:52096800-52098200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr19:52096800-52098400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr19:52096800-52098400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr19:52096800-52098400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:52096800-52098400	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr19:52096800-52098400	Active TSS	Fetal Intestine Large	intestine
20	chr19:52096800-52098400	Active TSS	Rectal Smooth Muscle	rectum
21	chr19:52096800-52098400	Active TSS	HSMMtube	muscle
22	chr19:52096800-52098600	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr19:52097000-52098200	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr19:52097000-52098200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:52097000-52098200	Active TSS	Aorta	Aorta
26	chr19:52097000-52098200	Active TSS	Right Ventricle	heart
27	chr19:52097000-52098200	Flanking Active TSS	HUVEC	blood vessel
28	chr19:52097000-52098400	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr19:52097000-52098400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:52097000-52098400	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr19:52097000-52098400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr19:52097000-52098400	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr19:52097000-52098400	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr19:52097000-52098400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr19:52097000-52098400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:52097000-52098400	Active TSS	Gastric	stomach
37	chr19:52097000-52098400	Active TSS	Psoas Muscle	Psoas
38	chr19:52097000-52098600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr19:52097000-52098600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr19:52097200-52098200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr19:52097200-52098200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:52097200-52098200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:52097200-52098200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:52097200-52098200	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr19:52097200-52098200	Active TSS	Brain Angular Gyrus	brain
46	chr19:52097200-52098200	Active TSS	Brain Anterior Caudate	brain
47	chr19:52097200-52098200	Active TSS	Brain Hippocampus Middle	brain
48	chr19:52097200-52098200	Active TSS	Brain Substantia Nigra	brain
49	chr19:52097200-52098200	Active TSS	Small Intestine	intestine
50	chr19:52097200-52098200	Active TSS	GM12878-XiMat	blood

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