Variant report

Variant	rs34603606
Chromosome Location	chr19:53062348-53062349
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	GATA2	chr19:53062024-53062555	K562	blood:	n/a	n/a
2	POLR2A	chr19:53061913-53062539	GM12878	blood:	n/a	n/a
3	SPI1	chr19:53062326-53062476	K562	blood:	n/a	n/a
4	USF1	chr19:53062084-53062377	H1-hESC	embryonic stem cell:	n/a	n/a
5	SPI1	chr19:53062344-53062485	K562	blood:	n/a	n/a
6	POLR2A	chr19:53061891-53062867	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr19:53062076-53062360	H1-hESC	embryonic stem cell:	n/a	n/a
8	USF1	chr19:53062096-53062353	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
RPL39P34	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12971372	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12977988	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12979584	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12985487	0.82[EUR][1000 genomes]
rs12986137	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2029316	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];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	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34106830	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34724169	0.98[EUR][1000 genomes]
rs34747259	0.93[EUR][1000 genomes]
rs34866464	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34942135	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35068231	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35888888	0.95[EUR][1000 genomes]
rs35990292	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35993483	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4401146	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55930753	0.86[ASN][1000 genomes]
rs60617297	0.86[ASN][1000 genomes]
rs61746334	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71358884	0.82[EUR][1000 genomes]
rs73578236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73578252	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73578286	0.86[ASN][1000 genomes]
rs73578289	0.86[ASN][1000 genomes]
rs8104197	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

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	chr19:53048000-53066400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
7	chr19:53049400-53063800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr19:53050400-53065400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
9	chr19:53050400-53069200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:53051000-53068000	ZNF genes & repeats	Fetal Intestine Large	intestine
11	chr19:53051400-53068200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
12	chr19:53051600-53068000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:53051600-53068200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
14	chr19:53051600-53073200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr19:53052000-53067400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
16	chr19:53052000-53067800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:53052200-53063400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
18	chr19:53052200-53067800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
19	chr19:53053600-53067800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
20	chr19:53054600-53064200	ZNF genes & repeats	Fetal Muscle Leg	muscle
21	chr19:53056200-53065800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:53056600-53065400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr19:53057200-53062800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
24	chr19:53057600-53064200	ZNF genes & repeats	Placenta	Placenta
25	chr19:53058400-53072600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:53058600-53065200	Weak transcription	Brain Substantia Nigra	brain
27	chr19:53058600-53070000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr19:53058600-53072800	Weak transcription	Fetal Brain Male	brain
29	chr19:53058800-53070000	Weak transcription	Hela-S3	cervix
30	chr19:53059000-53064600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr19:53059000-53068000	Strong transcription	Dnd41	blood
32	chr19:53059000-53068600	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr19:53059200-53062400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr19:53059200-53073000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:53059400-53062600	Weak transcription	Brain Germinal Matrix	brain
36	chr19:53059400-53065600	ZNF genes & repeats	Fetal Stomach	stomach
37	chr19:53059800-53066600	ZNF genes & repeats	Colonic Mucosa	Colon
38	chr19:53060200-53064000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
39	chr19:53060200-53064200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:53060200-53067400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
41	chr19:53060400-53065400	ZNF genes & repeats	Primary B cells from cord blood	blood
42	chr19:53060600-53062400	Strong transcription	Fetal Kidney	kidney
43	chr19:53060800-53062600	Strong transcription	Ovary	ovary
44	chr19:53060800-53062800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:53060800-53064000	Weak transcription	Psoas Muscle	Psoas
46	chr19:53060800-53067200	ZNF genes & repeats	Lung	lung
47	chr19:53060800-53068600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:53060800-53069400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:53060800-53072800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr19:53061000-53072600	Weak transcription	Fetal Brain Female	brain

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