Variant report

Variant	rs2302485
Chromosome Location	chr19:42741124-42741125
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:42740960-42741364	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr19:42740834-42741155	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:42740707-42741610	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:42740902-42741299	K562	blood:	n/a	n/a
5	POLR2A	chr19:42739227-42741345	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr19:42732840-42741292	K562	blood:	n/a	n/a
7	POLR2A	chr19:42741050-42741275	K562	blood:	n/a	n/a
8	POLR2A	chr19:42740742-42741241	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:42739329-42741220	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr19:42741053-42741253	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr19:42740912-42741260	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:42739869-42741325	K562	blood:	n/a	n/a
13	POLR2A	chr19:42741102-42741140	MCF-7	breast:	n/a	n/a
14	POLR2A	chr19:42740095-42741145	HL-60	blood:	n/a	n/a
15	POLR2A	chr19:42740847-42741250	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42634611..42641780-chr19:42741001..42747645,8	MCF-7	breast:
2	chr19:42740377..42742474-chr19:42805316..42808088,2	K562	blood:
3	chr19:42722405..42725200-chr19:42739571..42741128,2	MCF-7	breast:
4	chr19:42740830..42743417-chr19:42815153..42817394,2	MCF-7	breast:

No data

Variant related genes	Relation type
GSK3A	TF binding region
ENSG00000028277	Chromatin interaction
ENSG00000167625	Chromatin interaction
ENSG00000188368	Chromatin interaction
ENSG00000079462	Chromatin interaction
ENSG00000254887	Chromatin interaction
ENSG00000266226	Chromatin interaction
ENSG00000160570	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10410185	0.82[CHB][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs10410198	0.82[CHB][hapmap];0.91[ASN][1000 genomes]
rs10410698	0.82[CHB][hapmap];0.91[ASN][1000 genomes]
rs10412833	0.82[ASN][1000 genomes]
rs10426306	0.91[ASN][1000 genomes]
rs10426310	0.91[ASN][1000 genomes]
rs10500285	0.86[GIH][hapmap]
rs11557114	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11878620	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11880124	0.86[GIH][hapmap]
rs11882654	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11883412	0.89[GIH][hapmap];0.80[MEX][hapmap]
rs1206009	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs1206027	0.82[CHB][hapmap]
rs1206029	0.82[CHB][hapmap];0.80[MEX][hapmap]
rs1206033	0.82[CHB][hapmap]
rs1206038	0.82[CHB][hapmap]
rs1206040	0.82[CHB][hapmap]
rs1206041	0.82[CHB][hapmap]
rs1206044	0.82[CHB][hapmap]
rs1209280	0.82[ASN][1000 genomes]
rs1211265	0.82[ASN][1000 genomes]
rs1613100	0.82[CHB][hapmap]
rs1654623	0.82[CHB][hapmap]
rs1676211	0.82[CHB][hapmap]
rs1676217	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs1676221	0.82[CHB][hapmap]
rs1676222	0.82[CHB][hapmap]
rs1685565	0.82[CHB][hapmap]
rs16975684	0.93[GIH][hapmap];0.80[MEX][hapmap]
rs17270169	0.86[GIH][hapmap];1.00[YRI][hapmap]
rs2267630	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2303652	0.93[GIH][hapmap];0.91[MEX][hapmap]
rs2537697	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs2615614	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs28537976	0.91[ASN][1000 genomes]
rs28621009	0.82[CHB][hapmap]
rs35493131	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3745231	0.93[GIH][hapmap];0.91[MEX][hapmap]
rs3745233	0.93[GIH][hapmap];0.91[MEX][hapmap]
rs3810148	0.82[CHB][hapmap];0.80[MEX][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3826705	0.86[GIH][hapmap]
rs4141062	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57938324	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61735151	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7248379	0.93[GIH][hapmap];0.80[MEX][hapmap]
rs7258795	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73552881	0.91[ASN][1000 genomes]
rs73552895	0.91[ASN][1000 genomes]
rs741070	0.82[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8182491	0.93[GIH][hapmap];0.80[MEX][hapmap]
rs851296	0.82[CHB][hapmap]
rs851612	0.87[ASN][1000 genomes]
rs851615	0.82[ASN][1000 genomes]
rs9636121	0.82[CHB][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats 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
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
7	nsv833833	chr19:42657276-42783122	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
9	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription 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	70 gene(s)	inside rSNPs	diseases
10	nsv833834	chr19:42736444-42835027	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	42 gene(s)	inside rSNPs	diseases
11	nsv911784	chr19:42741124-42787664	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
12	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42725000-42747000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:42725400-42745200	Weak transcription	Fetal Brain Male	brain
3	chr19:42725600-42744000	Weak transcription	Right Atrium	heart
4	chr19:42725600-42745000	Weak transcription	Fetal Heart	heart
5	chr19:42726400-42741600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:42726600-42741400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:42726800-42741200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr19:42726800-42744000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr19:42726800-42745000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:42727000-42745000	Weak transcription	Hela-S3	cervix
11	chr19:42728200-42741400	Strong transcription	Fetal Lung	lung
12	chr19:42728200-42744000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:42728400-42741200	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr19:42728400-42741200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr19:42728400-42741200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr19:42728400-42741200	Strong transcription	Liver	Liver
17	chr19:42728400-42741200	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr19:42728400-42741200	Strong transcription	Fetal Brain Female	brain
19	chr19:42728400-42741200	Strong transcription	Left Ventricle	heart
20	chr19:42728400-42741200	Strong transcription	Lung	lung
21	chr19:42728400-42741200	Strong transcription	Rectal Smooth Muscle	rectum
22	chr19:42728400-42741400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:42728400-42741400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:42728400-42741400	Strong transcription	Brain Germinal Matrix	brain
25	chr19:42728400-42741400	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr19:42728400-42741600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr19:42728400-42741800	Strong transcription	Primary T cells from cord blood	blood
28	chr19:42728400-42741800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr19:42728400-42742000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr19:42728400-42743200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr19:42728400-42743600	Strong transcription	Dnd41	blood
32	chr19:42728400-42744800	Strong transcription	Fetal Thymus	thymus
33	chr19:42728600-42741400	Strong transcription	Primary B cells from cord blood	blood
34	chr19:42728600-42741600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr19:42728600-42744400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr19:42731200-42741200	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr19:42731200-42741400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr19:42731400-42741200	Strong transcription	NH-A	brain
39	chr19:42731400-42741400	Strong transcription	Osteobl	bone
40	chr19:42731400-42741600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr19:42731400-42744600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr19:42731600-42744000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:42732000-42741400	Strong transcription	NHEK	skin
44	chr19:42732200-42743200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:42732600-42741200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr19:42733000-42741200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr19:42733000-42741400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:42733200-42741200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr19:42733200-42741200	Strong transcription	Esophagus	oesophagus
50	chr19:42733600-42741200	Strong transcription	Spleen	Spleen

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