Variant report

Variant	rs17619980
Chromosome Location	chr12:21590490-21590491
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:435)
CpG islands
(count:183)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:435 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ETS1	chr12:21590347-21591243	A549	lung:	n/a	chr12:21590569-21590578 chr12:21590569-21590578 chr12:21590569-21590578 chr12:21590566-21590579 chr12:21590570-21590580 chr12:21590569-21590578 chr12:21590569-21590578 chr12:21590565-21590581 chr12:21590566-21590581 chr12:21590569-21590578 chr12:21590569-21590578
2	RAD21	chr12:21590315-21591051	A549	lung:	n/a	chr12:21590597-21590609
3	STAT5A	chr12:21590306-21591031	GM12878	blood:	n/a	chr12:21590818-21590830
4	TCF7L2	chr12:21590417-21591318	HCT-116	colon:	n/a	n/a
5	ELF1	chr12:21590166-21591475	HCT-116	colon:	n/a	chr12:21590837-21590848 chr12:21590837-21590848
6	MYC	chr12:21590315-21591413	K562	blood:	n/a	n/a
7	RAD21	chr12:21590404-21590807	HepG2	liver:	n/a	chr12:21590597-21590609
8	POLR2A	chr12:21590107-21592828	GM12878	blood:	n/a	n/a
9	MAX	chr12:21590279-21591077	SK-N-SH	brain:	n/a	n/a
10	MAZ	chr12:21590266-21591060	Hela-S3	cervix:	n/a	n/a
11	CEBPB	chr12:21590431-21591337	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr12:21590176-21591363	A549	lung:	n/a	n/a
13	ELK4	chr12:21590318-21591005	Hela-S3	cervix:	n/a	chr12:21590568-21590579 chr12:21590569-21590578 chr12:21590569-21590577
14	MYBL2	chr12:21590356-21590837	HepG2	liver:	n/a	n/a
15	ZNF143	chr12:21590428-21590874	H1-hESC	embryonic stem cell:	n/a	n/a
16	USF2	chr12:21590363-21591086	Hela-S3	cervix:	n/a	n/a
17	GABPA	chr12:21590435-21590865	HepG2	liver:	n/a	n/a
18	POLR2A	chr12:21590323-21591383	GM18951	blood:	n/a	n/a
19	E2F6	chr12:21590391-21591198	K562	blood:	n/a	n/a
20	CHD2	chr12:21590385-21590931	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr12:21590335-21591496	GM18526	blood:	n/a	n/a
22	SP1	chr12:21590250-21591439	A549	lung:	n/a	chr12:21590816-21590830 chr12:21590676-21590687
23	POLR2A	chr12:21590320-21591381	GM12878	blood:	n/a	n/a
24	CREB1	chr12:21590424-21590988	H1-hESC	embryonic stem cell:	n/a	n/a
25	STAT1	chr12:21590361-21591030	GM12878	blood:	n/a	chr12:21590818-21590830
26	POLR2A	chr12:21590320-21591496	K562	blood:	n/a	n/a
27	PML	chr12:21590247-21590950	K562	blood:	n/a	chr12:21590929-21590937
28	ELF1	chr12:21590397-21591008	K562	blood:	n/a	chr12:21590837-21590848 chr12:21590837-21590848
29	TBP	chr12:21590365-21591061	HepG2	liver:	n/a	n/a
30	YY1	chr12:21590458-21590889	GM12891	blood:	n/a	chr12:21590660-21590672
31	JUND	chr12:21590349-21590901	A549	lung:	n/a	n/a
32	FOXM1	chr12:21590375-21591229	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:21590173-21591324	U87	brain:	n/a	n/a
34	POLR2A	chr12:21590147-21591406	Raji	blood:	n/a	n/a
35	CTCF	chr12:21590440-21590590	RPTEC	kidney:	n/a	n/a
36	NRF1	chr12:21590482-21591021	GM12878	blood:	n/a	n/a
37	POLR2A	chr12:21590338-21591038	GM12892	blood:	n/a	n/a
38	ELK1	chr12:21590415-21590749	K562	blood:	n/a	chr12:21590569-21590578 chr12:21590569-21590578
39	POLR2A	chr12:21590402-21591052	SK-N-SH	brain:	n/a	n/a
40	TEAD4	chr12:21590405-21590918	H1-hESC	embryonic stem cell:	n/a	n/a
41	TBP	chr12:21590197-21591519	H1-hESC	embryonic stem cell:	n/a	n/a
42	TAF1	chr12:21590369-21591025	K562	blood:	n/a	n/a
43	POLR2A	chr12:21590310-21591494	GM18505	blood:	n/a	n/a
44	POLR2A	chr12:21590376-21591017	GM12878	blood:	n/a	n/a
45	ELF1	chr12:21590369-21591430	GM12878	blood:	n/a	chr12:21590837-21590848 chr12:21590837-21590848
46	REST	chr12:21590157-21591174	A549	lung:	n/a	n/a
47	GATA1	chr12:21590101-21591012	PBDE	blood:	n/a	n/a
48	TAF1	chr12:21590386-21590850	GM12892	blood:	n/a	n/a
49	MYC	chr12:21590294-21591242	MCF10A-Er-Src	breast:	n/a	n/a
50	GABPA	chr12:21590390-21590875	Hela-S3	cervix:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:21590451-21590501	HNPCEpiC	eye:	n/a
2	chr12:21590480-21590530	SAEC	small airway:	n/a
3	chr12:21590470-21590520	GM12891	blood:	n/a
4	chr12:21590470-21590520	ProgFib	skin:	n/a
5	chr12:21590451-21590501	IMR90	lung:	fetal
6	chr12:21590480-21590530	PrEC	prostate:	n/a
7	chr12:21590480-21590530	HCPEpiC	choroid plexus:	n/a
8	chr12:21590470-21590520	CMK	blood:	n/a
9	chr12:21590470-21590520	GM12878	blood:	n/a
10	chr12:21590451-21590501	NB4	blood:	n/a
11	chr12:21590480-21590530	HCM	heart:	n/a
12	chr12:21590451-21590501	HPAEpiC	pulmonary alveolar:	n/a
13	chr12:21590451-21590501	Hela-S3	cervix:	n/a
14	chr12:21590470-21590520	HEK293	kidney:	embryo
15	chr12:21590480-21590530	BJ	skin:	n/a
16	chr12:21590480-21590530	NB4	blood:	n/a
17	chr12:21590480-21590530	AoSMC	blood vessel:	n/a
18	chr12:21590451-21590501	NH-A	brain:	n/a
19	chr12:21590470-21590520	NHBE	bronchial:	n/a
20	chr12:21590480-21590530	K562	blood:	n/a
21	chr12:21590470-21590520	HNPCEpiC	eye:	n/a
22	chr12:21590451-21590501	HCM	heart:	n/a
23	chr12:21590451-21590501	U87	brain:	n/a
24	chr12:21590451-21590501	GM12878	blood:	n/a
25	chr12:21590480-21590530	LNCaP	prostate:	n/a
26	chr12:21590480-21590530	HCT-116	colon:	n/a
27	chr12:21590480-21590530	HRPEpiC	eye:	n/a
28	chr12:21590451-21590501	AG10803	skin:	n/a
29	chr12:21590470-21590520	Jurkat	blood:	n/a
30	chr12:21590480-21590530	NT2-D1	testis:	n/a
31	chr12:21590451-21590501	PFSK-1	brain:	n/a
32	chr12:21590451-21590501	HCPEpiC	choroid plexus:	n/a
33	chr12:21590451-21590501	T-47D	breast:	n/a
34	chr12:21590470-21590520	MCF10A-Er-Src	breast:	n/a
35	chr12:21590480-21590530	CMK	blood:	n/a
36	chr12:21590470-21590520	HAEpiC	amniotic membrane:	n/a
37	chr12:21590470-21590520	HEEpiC	esophagus:	n/a
38	chr12:21590470-21590520	HMEC	breast:	n/a
39	chr12:21590480-21590530	Hela-S3	cervix:	n/a
40	chr12:21590480-21590530	GM12891	blood:	n/a
41	chr12:21590480-21590530	HPAEpiC	pulmonary alveolar:	n/a
42	chr12:21590470-21590520	HCT-116	colon:	n/a
43	chr12:21590480-21590530	NHBE	bronchial:	n/a
44	chr12:21590480-21590530	HL-60	blood:	n/a
45	chr12:21590480-21590530	AG09319	gingival:	n/a
46	chr12:21590451-21590501	PrEC	prostate:	n/a
47	chr12:21590470-21590520	PANC-1	pancreas:	n/a
48	chr12:21590480-21590530	GM06990	blood:	n/a
49	chr12:21590451-21590501	NHBE	bronchial:	n/a
50	chr12:21590480-21590530	RPTEC	kidney:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:21569338..21572113-chr12:21589171..21592854,4	K562	blood:
2	chr12:21569338..21572113-chr12:21589171..21592483,4	K562	blood:
3	chr12:21590034..21590802-chr19:47760711..47761229,2	Hela-S3	cervix:
4	chr11:106698243..106699219-chr12:21590223..21591148,2	HCT-116	colon:
5	chr12:21590441..21591053-chr3:42054547..42055346,2	NB4	blood:
6	chr11:30344192..30345102-chr12:21590448..21591163,2	Hela-S3	cervix:
7	chr12:21589456..21592020-chr12:21808889..21812230,4	K562	blood:
8	chr11:85780118..85780978-chr12:21590354..21590877,2	Hela-S3	cervix:
9	chr12:21590241..21590802-chr3:49058409..49058917,2	NB4	blood:

No data

Variant related genes	Relation type
PYROXD1	TF binding region
PYROXD1	CpG island
ENSG00000084453	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000073921	Chromatin interaction
ENSG00000105321	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000213252	Chromatin interaction
ENSG00000152219	Chromatin interaction
ENSG00000111716	Chromatin interaction
ENSG00000182606	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10492116	1.00[CEU][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17619644	1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17620142	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17681644	1.00[MEX][hapmap];0.84[YRI][hapmap]
rs17682057	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17682270	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57595949	0.88[AFR][1000 genomes]
rs58874042	0.80[AFR][1000 genomes]
rs7133812	0.84[YRI][hapmap]
rs71537696	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71582885	0.89[EUR][1000 genomes]
rs7304732	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73246509	0.88[AFR][1000 genomes]
rs73246585	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73248030	0.80[AFR][1000 genomes]
rs73249910	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74067190	0.80[AFR][1000 genomes]
rs74067201	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526789	chr12:21555691-21590788	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv898895	chr12:21561645-21621891	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv469163	chr12:21579080-21592357	Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
7	nsv557742	chr12:21579080-21592357	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 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	chr12:21589800-21591400	Active TSS	Fetal Kidney	kidney
2	chr12:21589800-21591600	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr12:21589800-21591600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:21589800-21591600	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr12:21589800-21591600	Active TSS	HSMMtube	muscle
6	chr12:21589800-21592000	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr12:21590000-21590600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr12:21590000-21590600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr12:21590000-21590600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:21590000-21590600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr12:21590000-21590800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:21590000-21591200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr12:21590000-21591200	Active TSS	Adipose Nuclei	Adipose
14	chr12:21590000-21591200	Active TSS	Liver	Liver
15	chr12:21590000-21591200	Active TSS	Fetal Brain Male	brain
16	chr12:21590000-21591200	Active TSS	Left Ventricle	heart
17	chr12:21590000-21591400	Active TSS	H9 Cell Line	embryonic stem cell
18	chr12:21590000-21591400	Active TSS	Brain Anterior Caudate	brain
19	chr12:21590000-21591400	Active TSS	Brain Hippocampus Middle	brain
20	chr12:21590000-21591400	Active TSS	Colon Smooth Muscle	Colon
21	chr12:21590000-21591400	Active TSS	Fetal Heart	heart
22	chr12:21590000-21591400	Active TSS	Fetal Intestine Large	intestine
23	chr12:21590000-21591600	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr12:21590000-21591600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:21590000-21591600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:21590000-21591600	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr12:21590000-21591600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:21590000-21591600	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr12:21590000-21591600	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr12:21590000-21591600	Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr12:21590000-21591600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:21590000-21591600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:21590000-21591600	Active TSS	Brain Angular Gyrus	brain
34	chr12:21590000-21591600	Active TSS	Colonic Mucosa	Colon
35	chr12:21590000-21591600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr12:21590000-21591600	Active TSS	Fetal Muscle Trunk	muscle
37	chr12:21590000-21591600	Active TSS	Placenta	Placenta
38	chr12:21590000-21591600	Active TSS	Ovary	ovary
39	chr12:21590000-21591600	Active TSS	Right Atrium	heart
40	chr12:21590000-21591600	Active TSS	NHDF-Ad	bronchial
41	chr12:21590000-21591600	Active TSS	NHEK	skin
42	chr12:21590000-21591800	Active TSS	H1 Cell Line	embryonic stem cell
43	chr12:21590000-21591800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:21590000-21591800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:21590000-21591800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:21590000-21591800	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr12:21590000-21591800	Active TSS	Fetal Intestine Small	intestine
48	chr12:21590000-21591800	Active TSS	Right Ventricle	heart
49	chr12:21590000-21591800	Active TSS	HSMM	muscle
50	chr12:21590000-21592000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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