Variant report

Variant	rs2288512
Chromosome Location	chr19:42409039-42409040
allele	C/T
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	chr19:42408250-42409108	A549	lung:	n/a	n/a
2	POLR2A	chr19:42408990-42409190	K562	blood:	n/a	n/a
3	POLR2A	chr19:42408903-42409093	HepG2	liver:	n/a	n/a
4	BCL3	chr19:42408126-42409257	A549	lung:	n/a	n/a
5	MAX	chr19:42408161-42409071	MCF-7	breast:	n/a	n/a
6	ELF1	chr19:42408234-42409094	MCF-7	breast:	n/a	n/a
7	FOXA2	chr19:42407796-42409477	HepG2	liver:	n/a	n/a
8	FOXA1	chr19:42408484-42409064	HepG2	liver:	n/a	chr19:42408723-42408738 chr19:42408747-42408762
9	TCF12	chr19:42407980-42409375	A549	lung:	n/a	chr19:42408794-42408803 chr19:42408749-42408758 chr19:42408728-42408737 chr19:42408174-42408184
10	SIN3AK20	chr19:42408169-42409315	MCF-7	breast:	n/a	n/a
11	MAX	chr19:42408113-42409175	A549	lung:	n/a	n/a
12	FOXA1	chr19:42408410-42409093	HepG2	liver:	n/a	chr19:42408723-42408738 chr19:42408747-42408762
13	FOXA2	chr19:42408219-42409219	A549	lung:	n/a	n/a
14	NR2F2	chr19:42408136-42409108	MCF-7	breast:	n/a	n/a
15	FOXA1	chr19:42408425-42409081	HepG2	liver:	n/a	chr19:42408723-42408738 chr19:42408747-42408762
16	FOSL2	chr19:42408353-42409186	A549	lung:	n/a	chr19:42408973-42408981
17	CEBPB	chr19:42408571-42409062	MCF-7	breast:	n/a	n/a
18	SP1	chr19:42408296-42409113	A549	lung:	n/a	chr19:42408674-42408686 chr19:42408854-42408864 chr19:42408666-42408680 chr19:42408674-42408686 chr19:42408854-42408864 chr19:42408316-42408325 chr19:42408676-42408685
19	POLR2A	chr19:42408747-42409147	K562	blood:	n/a	n/a
20	NR3C1	chr19:42408539-42409051	A549	lung:	n/a	chr19:42408559-42408572 chr19:42408935-42408953
21	MYBL2	chr19:42408506-42409051	HepG2	liver:	n/a	n/a
22	TEAD4	chr19:42408504-42409064	HepG2	liver:	n/a	n/a
23	SP1	chr19:42408117-42409775	A549	lung:	n/a	chr19:42409456-42409470 chr19:42408674-42408686 chr19:42408854-42408864 chr19:42408666-42408680 chr19:42408674-42408686 chr19:42408854-42408864 chr19:42408316-42408325 chr19:42408676-42408685
24	EP300	chr19:42408387-42409178	A549	lung:	n/a	n/a
25	ZEB1	chr19:42408521-42409043	HepG2	liver:	n/a	n/a
26	EP300	chr19:42408526-42409041	HepG2	liver:	n/a	n/a
27	FOXA2	chr19:42408348-42409250	A549	lung:	n/a	n/a
28	MAX	chr19:42408223-42409113	MCF-7	breast:	n/a	n/a
29	EP300	chr19:42408359-42409088	A549	lung:	n/a	n/a
30	ZEB1	chr19:42408269-42409275	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42386056..42389793-chr19:42407267..42411147,5	MCF-7	breast:
2	chr19:42406370..42409595-chr19:42409748..42413169,6	K562	blood:
3	chr19:42403036..42406958-chr19:42407264..42409613,3	MCF-7	breast:
4	chr19:42385733..42387603-chr19:42407160..42410354,3	MCF-7	breast:
5	chr19:42364075..42365757-chr19:42408269..42410021,2	K562	blood:
6	chr19:42407772..42411584-chr19:42411987..42415149,3	MCF-7	breast:
7	chr19:42406489..42409925-chr19:42413611..42416710,4	K562	blood:
8	chr19:42362818..42366371-chr19:42406679..42410305,7	MCF-7	breast:

Variant related genes	Relation type
ARHGEF1	TF binding region
ENSG00000105372	Chromatin interaction
ENSG00000268041	Chromatin interaction
ENSG00000076928	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10401189	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10401937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10402667	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10403081	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10417495	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10419314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11083638	1.00[CEU][hapmap]
rs11083640	1.00[CEU][hapmap]
rs11878536	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11878555	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs11878734	1.00[CEU][hapmap]
rs11878811	1.00[CEU][hapmap]
rs11879437	1.00[CEU][hapmap]
rs11880977	1.00[CEU][hapmap]
rs11881323	1.00[CEU][hapmap]
rs11883018	1.00[CEU][hapmap]
rs12104228	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16975619	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2288509	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2288510	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2288511	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2303798	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28396197	0.93[AMR][1000 genomes]
rs28521795	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28706300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3745222	0.97[CHD][hapmap];1.00[JPT][hapmap]
rs6509003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs717225	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7252790	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252800	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7253691	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7260129	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs73550603	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73550610	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73550618	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8109784	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8109959	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8110305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8113339	1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8113686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs891169	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs891170	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs891171	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs891172	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9653098	1.00[CEU][hapmap]
rs9989667	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	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
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	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
8	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42389200-42429200	Weak transcription	Right Atrium	heart
2	chr19:42389400-42411400	Weak transcription	Fetal Brain Male	brain
3	chr19:42390800-42411200	Weak transcription	Hela-S3	cervix
4	chr19:42392000-42412600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr19:42392000-42412600	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:42392000-42412600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:42392200-42412400	Strong transcription	Fetal Muscle Leg	muscle
8	chr19:42392200-42412800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr19:42392400-42410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:42392400-42412400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:42392400-42413200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:42392600-42411800	Strong transcription	Placenta	Placenta
13	chr19:42392600-42413600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr19:42393400-42413600	Strong transcription	Thymus	Thymus
15	chr19:42393800-42413000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:42394000-42413000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:42395600-42412400	Strong transcription	Right Ventricle	heart
18	chr19:42395800-42411600	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr19:42395800-42411800	Strong transcription	Fetal Brain Female	brain
20	chr19:42396000-42411800	Strong transcription	Brain Hippocampus Middle	brain
21	chr19:42396000-42412000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr19:42396800-42415200	Strong transcription	Dnd41	blood
23	chr19:42397400-42411600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:42397400-42413600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:42397600-42412800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr19:42398000-42411200	Strong transcription	Primary B cells from cord blood	blood
27	chr19:42398000-42411400	Strong transcription	Aorta	Aorta
28	chr19:42398000-42411400	Strong transcription	Esophagus	oesophagus
29	chr19:42398800-42412600	Strong transcription	Spleen	Spleen
30	chr19:42398800-42414000	Strong transcription	Fetal Thymus	thymus
31	chr19:42400200-42412400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr19:42400400-42411600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr19:42401600-42411400	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr19:42401800-42410000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:42401800-42410600	Strong transcription	Brain Anterior Caudate	brain
36	chr19:42401800-42410800	Strong transcription	NH-A	brain
37	chr19:42401800-42411000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:42401800-42411000	Strong transcription	NHEK	skin
39	chr19:42401800-42411400	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr19:42401800-42411800	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr19:42401800-42412400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:42401800-42412600	Strong transcription	Ovary	ovary
43	chr19:42402000-42410400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:42402000-42410400	Strong transcription	GM12878-XiMat	blood
45	chr19:42402000-42411800	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr19:42402200-42409400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:42402200-42410400	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr19:42402200-42411800	Strong transcription	Brain Substantia Nigra	brain
49	chr19:42402200-42412000	Strong transcription	Primary T cells from cord blood	blood
50	chr19:42402400-42411400	Strong transcription	Brain Angular Gyrus	brain

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