Variant report

Variant	rs12971372
Chromosome Location	chr19:53059830-53059831
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11879684	1.00[ASN][1000 genomes]
rs11882311	1.00[ASN][1000 genomes]
rs12461522	1.00[ASN][1000 genomes]
rs12462080	1.00[ASN][1000 genomes]
rs12977988	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979584	0.84[EUR][1000 genomes]
rs12985487	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12986137	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16983943	1.00[ASN][1000 genomes]
rs2029316	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2061355	1.00[ASN][1000 genomes]
rs28570374	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329948	1.00[ASN][1000 genomes]
rs329949	1.00[ASN][1000 genomes]
rs34066730	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34106830	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34203482	1.00[ASN][1000 genomes]
rs34316627	1.00[ASN][1000 genomes]
rs34529833	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34603606	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34724169	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34747259	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34866464	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34942135	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35068231	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35356792	1.00[ASN][1000 genomes]
rs35591322	1.00[ASN][1000 genomes]
rs35888888	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35895760	1.00[ASN][1000 genomes]
rs35904532	1.00[ASN][1000 genomes]
rs35990292	0.84[EUR][1000 genomes]
rs35993483	0.84[EUR][1000 genomes]
rs36089907	1.00[ASN][1000 genomes]
rs382838	1.00[ASN][1000 genomes]
rs436426	1.00[ASN][1000 genomes]
rs4401146	0.84[EUR][1000 genomes]
rs557496	1.00[ASN][1000 genomes]
rs58067500	1.00[ASN][1000 genomes]
rs58494379	1.00[ASN][1000 genomes]
rs61545816	1.00[ASN][1000 genomes]
rs61746334	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71358875	1.00[ASN][1000 genomes]
rs71358876	1.00[ASN][1000 genomes]
rs71358877	1.00[ASN][1000 genomes]
rs71358878	1.00[ASN][1000 genomes]
rs71358879	1.00[ASN][1000 genomes]
rs71358884	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252479	1.00[ASN][1000 genomes]
rs7257824	1.00[ASN][1000 genomes]
rs73578236	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73578252	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590059	1.00[ASN][1000 genomes]
rs73934854	1.00[ASN][1000 genomes]
rs8104197	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811920	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1065584	chr19:53043126-53127459	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53042000-53070400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:53042200-53068200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr19:53042600-53061200	ZNF genes & repeats	Liver	Liver
4	chr19:53044800-53061200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:53046400-53069200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr19:53047400-53068200	ZNF genes & repeats	Thymus	Thymus
7	chr19:53047800-53068600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr19:53048000-53066400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
9	chr19:53048600-53061200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
10	chr19:53049400-53063800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr19:53049600-53060400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
12	chr19:53050400-53065400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
13	chr19:53050400-53069200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:53050600-53061200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:53050800-53061200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:53051000-53061400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
17	chr19:53051000-53068000	ZNF genes & repeats	Fetal Intestine Large	intestine
18	chr19:53051200-53061200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
19	chr19:53051400-53068200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
20	chr19:53051600-53061200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:53051600-53061200	ZNF genes & repeats	Adipose Nuclei	Adipose
22	chr19:53051600-53061400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:53051600-53061600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:53051600-53068000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:53051600-53068200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
26	chr19:53051600-53073200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:53052000-53067400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
28	chr19:53052000-53067800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:53052200-53063400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
30	chr19:53052200-53067800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
31	chr19:53053600-53067800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
32	chr19:53054000-53060000	ZNF genes & repeats	Fetal Lung	lung
33	chr19:53054200-53061200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
34	chr19:53054200-53061200	ZNF genes & repeats	Left Ventricle	heart
35	chr19:53054600-53061000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
36	chr19:53054600-53064200	ZNF genes & repeats	Fetal Muscle Leg	muscle
37	chr19:53055200-53061200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
38	chr19:53055800-53061200	ZNF genes & repeats	HMEC	breast
39	chr19:53056000-53061400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
40	chr19:53056200-53065800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:53056400-53060800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:53056600-53065400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:53057000-53061200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr19:53057200-53061400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
45	chr19:53057200-53062800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
46	chr19:53057600-53060800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:53057600-53064200	ZNF genes & repeats	Placenta	Placenta
48	chr19:53058400-53072600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:53058600-53060000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr19:53058600-53060200	Weak transcription	Pancreas	Pancrea

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