Variant report

Variant	rs12972894
Chromosome Location	chr19:19292047-19292048
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	POLR2A	chr19:19291708-19292096	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:19291895-19292090	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19286456..19293705-chr19:19298673..19304955,13	K562	blood:
2	chr19:19291248..19293065-chr19:19301550..19303514,2	K562	blood:
3	chr19:19291680..19293828-chr19:19294510..19298396,4	K562	blood:
4	chr19:19291324..19295055-chr19:19301522..19304242,3	MCF-7	breast:

Variant related genes	Relation type
MEF2BNB	TF binding region
ENSG00000213999	Chromatin interaction
ENSG00000064489	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000254901	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1005980	0.89[ASN][1000 genomes]
rs10417796	0.82[EUR][1000 genomes]
rs10418053	0.82[EUR][1000 genomes]
rs1050544	0.80[EUR][1000 genomes]
rs10854008	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10854009	0.81[EUR][1000 genomes]
rs10854012	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11669408	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11669860	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12609573	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12974672	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12975253	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12975290	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12980269	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12980955	0.81[EUR][1000 genomes]
rs12981160	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1858846	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2238668	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239369	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2239370	0.83[EUR][1000 genomes]
rs2283623	0.81[EUR][1000 genomes]
rs2314035	0.82[EUR][1000 genomes]
rs35342977	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3787040	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808185	0.84[EUR][1000 genomes]
rs539	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62135499	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71332145	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7250650	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256811	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7260127	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72997174	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs741706	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8101388	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active 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	39 gene(s)	inside rSNPs	diseases
3	nsv933613	chr19:19291456-19312244	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19277400-19300600	Weak transcription	Small Intestine	intestine
2	chr19:19280800-19301600	Weak transcription	NHEK	skin
3	chr19:19281400-19292200	Weak transcription	HMEC	breast
4	chr19:19281400-19300800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:19281600-19293000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:19281600-19297200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:19281600-19299400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr19:19281600-19300600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:19281600-19302000	Weak transcription	NH-A	brain
10	chr19:19281600-19302200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:19281800-19300000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:19281800-19301200	Weak transcription	Stomach Mucosa	stomach
13	chr19:19282000-19292200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:19282000-19301600	Weak transcription	Fetal Heart	heart
15	chr19:19283000-19292200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:19283400-19292200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:19283400-19300600	Weak transcription	Psoas Muscle	Psoas
18	chr19:19283400-19301600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:19283400-19302000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr19:19283400-19302200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:19283600-19301800	Weak transcription	HSMMtube	muscle
22	chr19:19283800-19292200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr19:19284200-19302000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:19285600-19301800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr19:19286000-19292800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr19:19286000-19301000	Weak transcription	HepG2	liver
27	chr19:19286000-19302000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr19:19286400-19294000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:19286600-19293600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:19286600-19293600	Strong transcription	Ovary	ovary
31	chr19:19286600-19293800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr19:19286600-19298200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:19286800-19293800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr19:19286800-19293800	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr19:19286800-19293800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr19:19286800-19294000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:19286800-19294000	Strong transcription	Stomach Smooth Muscle	stomach
38	chr19:19286800-19296600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr19:19287000-19293600	Strong transcription	Gastric	stomach
40	chr19:19287000-19293800	Strong transcription	Pancreas	Pancrea
41	chr19:19287000-19293800	Strong transcription	Thymus	Thymus
42	chr19:19287000-19294000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr19:19287000-19294400	Strong transcription	Primary T cells from cord blood	blood
44	chr19:19287200-19293400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr19:19287200-19293800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr19:19287200-19293800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr19:19287200-19293800	Strong transcription	Dnd41	blood
48	chr19:19287200-19294000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr19:19287200-19294000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:19287200-19294000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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