Variant report

Variant	rs2657930
Chromosome Location	chr19:52772768-52772769
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	E2F6	chr19:52772530-52773429	A549	lung:	n/a	chr19:52772776-52772785 chr19:52773100-52773114 chr19:52773093-52773100 chr19:52773093-52773100 chr19:52773093-52773100
2	SP1	chr19:52772355-52773208	HCT-116	colon:	n/a	chr19:52772796-52772806 chr19:52772735-52772746 chr19:52772774-52772786 chr19:52772775-52772784 chr19:52772774-52772786
3	SP1	chr19:52772432-52773073	H1-hESC	embryonic stem cell:	n/a	chr19:52772796-52772806 chr19:52772735-52772746 chr19:52772774-52772786 chr19:52772775-52772784 chr19:52772774-52772786
4	CEBPB	chr19:52772548-52773198	A549	lung:	n/a	chr19:52772693-52772710
5	POLR2A	chr19:52772457-52773698	MCF10A-Er-Src	breast:	n/a	n/a
6	ELF1	chr19:52772451-52773560	MCF-7	breast:	n/a	chr19:52772842-52772851 chr19:52772841-52772852 chr19:52772841-52772852
7	ZBTB7A	chr19:52772743-52772907	K562	blood:	n/a	n/a
8	POLR2A	chr19:52772517-52773433	HUVEC	blood vessel:	n/a	n/a
9	MAX	chr19:52772498-52773456	NB4	blood:	n/a	n/a
10	CEBPB	chr19:52772464-52773135	HCT-116	colon:	n/a	chr19:52772693-52772710
11	RUNX3	chr19:52772468-52773650	GM12878	blood:	n/a	n/a
12	CEBPB	chr19:52772517-52773338	IMR90	lung:	n/a	chr19:52772693-52772710
13	USF1	chr19:52772538-52773189	A549	lung:	n/a	chr19:52772825-52772841
14	POLR2A	chr19:52772358-52773879	MCF-7	breast:	n/a	n/a
15	SPI1	chr19:52772570-52772991	GM12891	blood:	n/a	chr19:52772736-52772749
16	POLR2A	chr19:52772393-52773418	HepG2	liver:	n/a	n/a
17	CEBPB	chr19:52772519-52773202	MCF-7	breast:	n/a	chr19:52772693-52772710
18	POLR2A	chr19:52772437-52773350	U87	brain:	n/a	n/a
19	CEBPB	chr19:52772489-52773112	ECC-1	luminal epithelium:	n/a	chr19:52772693-52772710
20	FOS	chr19:52772695-52772998	MCF10A-Er-Src	breast:	n/a	chr19:52772777-52772786
21	SP1	chr19:52772439-52773221	A549	lung:	n/a	chr19:52772796-52772806 chr19:52772735-52772746 chr19:52772774-52772786 chr19:52772775-52772784 chr19:52772774-52772786
22	HEY1	chr19:52772491-52773337	HepG2	liver:	n/a	chr19:52773224-52773239
23	ELF1	chr19:52772585-52773350	K562	blood:	n/a	chr19:52772842-52772851 chr19:52772841-52772852 chr19:52772841-52772852
24	MAX	chr19:52772359-52773723	A549	lung:	n/a	n/a
25	POLR2A	chr19:52772492-52773884	Hela-S3	cervix:	n/a	n/a
26	MYC	chr19:52772629-52773017	HepG2	liver:	n/a	n/a
27	MAX	chr19:52772544-52773256	K562	blood:	n/a	n/a
28	SIN3AK20	chr19:52772677-52773018	PFSK-1	brain:	n/a	n/a
29	POU2F2	chr19:52772432-52773410	GM12878	blood:	n/a	chr19:52772495-52772516 chr19:52772500-52772511
30	CEBPB	chr19:52772602-52773112	HepG2	liver:	n/a	chr19:52772693-52772710
31	CHD2	chr19:52772665-52772979	K562	blood:	n/a	n/a
32	CREB1	chr19:52772474-52773299	HepG2	liver:	n/a	n/a
33	CREB1	chr19:52772599-52773030	A549	lung:	n/a	n/a
34	POLR2A	chr19:52772454-52773872	GM18526	blood:	n/a	n/a
35	TAF1	chr19:52772577-52773206	GM12892	blood:	n/a	n/a
36	GABPA	chr19:52772575-52773037	K562	blood:	n/a	chr19:52772776-52772785
37	YY1	chr19:52772647-52773449	SK-N-SH	brain:	n/a	chr19:52773129-52773138 chr19:52773228-52773239
38	CEBPB	chr19:52772574-52772968	HepG2	liver:	n/a	chr19:52772693-52772710
39	MAX	chr19:52772596-52773174	HepG2	liver:	n/a	n/a
40	MAZ	chr19:52772597-52773669	K562	blood:	n/a	n/a
41	GABPA	chr19:52772576-52773104	MCF-7	breast:	n/a	chr19:52772776-52772785
42	SIN3AK20	chr19:52772744-52772995	K562	blood:	n/a	n/a
43	MAZ	chr19:52772452-52773315	GM12878	blood:	n/a	n/a
44	E2F6	chr19:52772602-52773297	K562	blood:	n/a	chr19:52772776-52772785 chr19:52773100-52773114 chr19:52773093-52773100 chr19:52773093-52773100 chr19:52773093-52773100
45	POLR2A	chr19:52772554-52773934	GM12891	blood:	n/a	n/a
46	POLR2A	chr19:52772401-52773496	Hela-S3	cervix:	n/a	n/a
47	NANOG	chr19:52772654-52772946	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr19:52772263-52774060	SK-N-MC	brain:	n/a	n/a
49	POLR2A	chr19:52772359-52773963	GM12892	blood:	n/a	n/a
50	MAX	chr19:52772456-52773450	ECC-1	luminal epithelium:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:52772724-52772774	ECC-1	luminal epithelium:	n/a
2	chr19:52772724-52772774	IMR90	lung:	fetal
3	chr19:52772724-52772774	HEEpiC	esophagus:	n/a
4	chr19:52772724-52772774	HL-60	blood:	n/a
5	chr19:52772724-52772774	A549	lung:	n/a
6	chr19:52772724-52772774	ovcar-3	ovarian:	n/a
7	chr19:52772724-52772774	T-47D	breast:	n/a
8	chr19:52772724-52772774	BE2_C	brain:	n/a
9	chr19:52772724-52772774	AG04450	lung:	fetal
10	chr19:52772724-52772774	HCT-116	colon:	n/a
11	chr19:52772724-52772774	MCF10A-Er-Src	breast:	n/a
12	chr19:52772724-52772774	CMK	blood:	n/a
13	chr19:52772724-52772774	NH-A	brain:	n/a
14	chr19:52772724-52772774	GM19239	blood:	n/a
15	chr19:52772724-52772774	HRPEpiC	eye:	n/a
16	chr19:52772724-52772774	SK-N-SH_RA	brain:	n/a
17	chr19:52772724-52772774	NHBE	bronchial:	n/a
18	chr19:52772724-52772774	SK-N-MC	brain:	n/a
19	chr19:52772724-52772774	MCF-7	breast:	n/a
20	chr19:52772724-52772774	AoSMC	blood vessel:	n/a
21	chr19:52772724-52772774	HNPCEpiC	eye:	n/a
22	chr19:52772724-52772774	NT2-D1	testis:	n/a
23	chr19:52772724-52772774	HRCEpiC	kidney:	n/a
24	chr19:52772724-52772774	AG10803	skin:	n/a
25	chr19:52772724-52772774	AG09319	gingival:	n/a
26	chr19:52772724-52772774	SAEC	small airway:	n/a
27	chr19:52772724-52772774	HCM	heart:	n/a
28	chr19:52772724-52772774	Hela-S3	cervix:	n/a
29	chr19:52772724-52772774	HEK293	kidney:	embryo
30	chr19:52772724-52772774	HepG2	liver:	n/a
31	chr19:52772724-52772774	Hepatocyte	liver:	n/a
32	chr19:52772724-52772774	GM06990	blood:	n/a
33	chr19:52772724-52772774	NHDF-neo	bronchial:	n/a
34	chr19:52772724-52772774	PrEC	prostate:	n/a
35	chr19:52772724-52772774	PANC-1	pancreas:	n/a
36	chr19:52772724-52772774	HAEpiC	amniotic membrane:	n/a
37	chr19:52772724-52772774	AG09309	skin:	n/a
38	chr19:52772724-52772774	ProgFib	skin:	n/a
39	chr19:52772724-52772774	RPTEC	kidney:	n/a
40	chr19:52772724-52772774	GM12891	blood:	n/a
41	chr19:52772724-52772774	GM12892	blood:	n/a
42	chr19:52772724-52772774	Caco-2	colon:	n/a
43	chr19:52772724-52772774	H1-hESC	embryonic stem cell:	embryo
44	chr19:52772724-52772774	HIPEpiC	eye:	n/a
45	chr19:52772724-52772774	HMEC	breast:	n/a
46	chr19:52772724-52772774	HCF	heart:	n/a
47	chr19:52772724-52772774	SK-N-SH	brain:	n/a
48	chr19:52772724-52772774	SKMC	muscle:	n/a
49	chr19:52772724-52772774	HPAEpiC	pulmonary alveolar:	n/a
50	chr19:52772724-52772774	U87	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52771242..52774496-chr19:52796154..52801198,5	MCF-7	breast:
2	chr19:52771473..52773658-chr19:52872286..52874915,2	MCF-7	breast:
3	chr19:52771349..52773088-chr19:52900874..52902470,2	MCF-7	breast:
4	chr19:52772712..52774263-chr19:52799047..52800693,2	K562	blood:
5	chr12:57039195..57039841-chr19:52772411..52773021,2	Hela-S3	cervix:
6	chr19:52772026..52776261-chr19:52781637..52786393,5	K562	blood:
7	chr19:52771880..52774244-chr19:52838831..52841718,3	MCF-7	breast:
8	chr11:62609126..62609696-chr19:52772249..52772925,2	NB4	blood:
9	chr19:52772363..52775107-chr19:52799601..52802037,4	MCF-7	breast:
10	chr19:52772381..52778282-chr19:52778346..52783668,9	MCF-7	breast:
11	chr19:52771362..52774263-chr19:52797982..52800693,2	K562	blood:
12	chr19:52733004..52735653-chr19:52772074..52774471,2	MCF-7	breast:
13	chr19:52772154..52772791-chr6:30709935..30710840,2	HCT-116	colon:
14	chr19:52641013..52643402-chr19:52771783..52774070,3	MCF-7	breast:
15	chr19:52771196..52774040-chr19:52836837..52839956,3	MCF-7	breast:
16	chr19:52597459..52600188-chr19:52771516..52774031,2	MCF-7	breast:

Variant related genes	Relation type
ZNF766	TF binding region
ZNF766	CpG island
ENSG00000196214	Chromatin interaction
ENSG00000110955	Chromatin interaction
ENSG00000208002	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000197608	Chromatin interaction
ENSG00000268015	Chromatin interaction
ENSG00000198464	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000221923	Chromatin interaction
ENSG00000256087	Chromatin interaction
ENSG00000269102	Chromatin interaction
ENSG00000269834	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000204611	Chromatin interaction
ENSG00000167555	Chromatin interaction
ENSG00000167554	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10404635	0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10425462	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10425644	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10426950	0.81[AFR][1000 genomes]
rs2089275	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560871	1.00[CHB][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560873	0.85[CHB][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560875	0.85[AFR][1000 genomes]
rs2560877	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657923	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657924	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657926	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657927	0.81[AFR][1000 genomes]
rs2657928	0.85[AFR][1000 genomes]
rs56211703	0.94[ASN][1000 genomes]
rs56369375	0.92[ASN][1000 genomes]
rs62110397	0.98[ASN][1000 genomes]
rs62110398	0.98[ASN][1000 genomes]
rs7255504	0.92[ASN][1000 genomes]
rs8107325	0.98[ASN][1000 genomes]
rs8113537	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs9304726	0.84[CHB][hapmap];0.92[ASN][1000 genomes]
rs9304727	0.83[LWK][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2657930	ZNF582	cis	parietal	SCAN
rs2657930	LAIR1	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52772200-52772800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr19:52772200-52772800	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr19:52772200-52772800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:52772200-52773000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr19:52772200-52773000	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr19:52772200-52773400	Active TSS	Primary T cells from cord blood	blood
7	chr19:52772200-52773600	Active TSS	Brain Angular Gyrus	brain
8	chr19:52772200-52773600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:52772200-52773800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:52772200-52773800	Active TSS	Brain Germinal Matrix	brain
11	chr19:52772200-52773800	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr19:52772200-52773800	Active TSS	Esophagus	oesophagus
13	chr19:52772200-52773800	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr19:52772200-52774000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr19:52772200-52774000	Active TSS	Fetal Lung	lung
16	chr19:52772200-52774200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:52772200-52774200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:52772200-52774200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:52772200-52774200	Active TSS	A549	lung
20	chr19:52772400-52772800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:52772400-52772800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr19:52772400-52772800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:52772400-52772800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:52772400-52772800	Flanking Active TSS	Liver	Liver
25	chr19:52772400-52772800	Enhancers	Stomach Mucosa	stomach
26	chr19:52772400-52772800	Active TSS	HepG2	liver
27	chr19:52772400-52773400	Active TSS	Brain Substantia Nigra	brain
28	chr19:52772400-52773600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:52772400-52773600	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr19:52772400-52773600	Active TSS	Hela-S3	cervix
31	chr19:52772400-52773600	Active TSS	HUVEC	blood vessel
32	chr19:52772400-52773800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr19:52772400-52773800	Active TSS	H1 Cell Line	embryonic stem cell
34	chr19:52772400-52773800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:52772400-52773800	Active TSS	Colon Smooth Muscle	Colon
36	chr19:52772400-52773800	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr19:52772400-52773800	Active TSS	Psoas Muscle	Psoas
38	chr19:52772400-52773800	Active TSS	Right Ventricle	heart
39	chr19:52772400-52773800	Active TSS	Thymus	Thymus
40	chr19:52772400-52773800	Active TSS	NHEK	skin
41	chr19:52772400-52774000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:52772400-52774000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:52772400-52774000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr19:52772400-52774000	Active TSS	Aorta	Aorta
45	chr19:52772400-52774000	Active TSS	Fetal Brain Male	brain
46	chr19:52772400-52774000	Active TSS	K562	blood
47	chr19:52772400-52774200	Active TSS	H9 Cell Line	embryonic stem cell
48	chr19:52772400-52774200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr19:52772400-52774200	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr19:52772400-52774200	Active TSS	Fetal Intestine Large	intestine

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