Variant report

Variant	rs12979584
Chromosome Location	chr19:53068196-53068197
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12327639	0.88[AFR][1000 genomes]
rs12327640	0.87[AFR][1000 genomes]
rs12971372	0.84[EUR][1000 genomes]
rs12977988	0.96[EUR][1000 genomes]
rs12985487	0.82[EUR][1000 genomes]
rs2029316	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061652	0.86[ASN][1000 genomes]
rs2447422	0.86[ASN][1000 genomes]
rs2931759	0.86[ASN][1000 genomes]
rs2931760	0.86[ASN][1000 genomes]
rs34066730	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34106830	0.96[EUR][1000 genomes]
rs34603606	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34724169	0.95[EUR][1000 genomes]
rs34747259	0.96[EUR][1000 genomes]
rs34866464	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34942135	0.93[EUR][1000 genomes]
rs35068231	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35888888	0.98[EUR][1000 genomes]
rs35990292	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35993483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4401146	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55930753	0.86[ASN][1000 genomes]
rs58875456	0.88[AFR][1000 genomes]
rs60617297	0.86[ASN][1000 genomes]
rs61746334	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71358884	0.82[EUR][1000 genomes]
rs73578236	0.84[EUR][1000 genomes]
rs73578252	0.96[EUR][1000 genomes]
rs73578286	0.86[ASN][1000 genomes]
rs73578289	0.86[ASN][1000 genomes]
rs8103262	0.81[AFR][1000 genomes]
rs8104197	0.87[EUR][1000 genomes]
rs8113404	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv458743	chr19:53065661-53114267	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv580027	chr19:53065661-53114267	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS 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	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 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	chr19:53046400-53069200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:53047400-53068200	ZNF genes & repeats	Thymus	Thymus
5	chr19:53047800-53068600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr19:53050400-53069200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:53051400-53068200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
8	chr19:53051600-53068200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
9	chr19:53051600-53073200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr19:53058400-53072600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:53058600-53070000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr19:53058600-53072800	Weak transcription	Fetal Brain Male	brain
13	chr19:53058800-53070000	Weak transcription	Hela-S3	cervix
14	chr19:53059000-53068600	ZNF genes & repeats	Fetal Intestine Small	intestine
15	chr19:53059200-53073000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:53060800-53068600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:53060800-53069400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr19:53060800-53072800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr19:53061000-53072600	Weak transcription	Fetal Brain Female	brain
20	chr19:53061000-53072800	Weak transcription	Brain Angular Gyrus	brain
21	chr19:53061200-53072600	Weak transcription	Fetal Heart	heart
22	chr19:53061200-53072800	Weak transcription	Brain Anterior Caudate	brain
23	chr19:53061400-53072600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:53062000-53068200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:53062000-53068800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:53062000-53070400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
27	chr19:53062000-53077800	ZNF genes & repeats	Liver	Liver
28	chr19:53062200-53072800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:53062400-53069800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr19:53062400-53072800	Weak transcription	Fetal Kidney	kidney
31	chr19:53062400-53073000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr19:53062600-53068200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:53062600-53069200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
34	chr19:53062800-53068600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr19:53063000-53072800	Weak transcription	Right Ventricle	heart
36	chr19:53063200-53068400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr19:53063200-53068600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr19:53063200-53068800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr19:53063200-53068800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr19:53063200-53068800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr19:53063200-53069800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr19:53063200-53070000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr19:53063400-53068600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:53063600-53073000	Weak transcription	HUVEC	blood vessel
45	chr19:53064000-53070400	Weak transcription	HSMMtube	muscle
46	chr19:53064000-53072800	Weak transcription	Brain Germinal Matrix	brain
47	chr19:53064200-53072200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr19:53064200-53073000	Weak transcription	Psoas Muscle	Psoas
49	chr19:53064400-53072400	Weak transcription	Osteobl	bone
50	chr19:53064800-53069800	Weak transcription	K562	blood

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