Variant report

Variant	rs55739939
Chromosome Location	chr5:37058632-37058633
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	chr5:37058614-37058677	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
NIPBL	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs55702678	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55712022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55886401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56065778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56272083	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs56332781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72732594	0.90[EUR][1000 genomes]
rs72732600	0.90[EUR][1000 genomes]
rs72732601	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs72734604	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs72734607	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs72734609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72734671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734681	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72734682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72734700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72734702	0.81[EUR][1000 genomes]
rs72736704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72736708	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72736710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72736712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72736713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72736714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72736717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72736721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72736723	0.81[EUR][1000 genomes]
rs72736727	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72736730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72736736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72736738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv1793961	chr5:36866835-37361728	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv530225	chr5:36886635-37331912	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1024051	chr5:36899712-37303001	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv537725	chr5:36899712-37303001	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv530226	chr5:36906377-37606367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv917880	chr5:36948778-37115342	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	esv1802391	chr5:36958598-37242600	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv597822	chr5:36997953-37147152	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv534064	chr5:37054962-37586210	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36949600-37086800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:36969800-37065000	Weak transcription	Stomach Mucosa	stomach
3	chr5:36991000-37064600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:36997600-37064600	Weak transcription	Esophagus	oesophagus
5	chr5:37001200-37066200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:37010800-37064600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:37012400-37064600	Weak transcription	Gastric	stomach
8	chr5:37014200-37066200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr5:37014200-37067200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr5:37019200-37060000	Weak transcription	Psoas Muscle	Psoas
11	chr5:37022400-37063600	Weak transcription	NHEK	skin
12	chr5:37027000-37066200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:37027600-37060000	Weak transcription	Small Intestine	intestine
14	chr5:37030800-37063800	Weak transcription	Fetal Brain Male	brain
15	chr5:37032200-37059400	Weak transcription	Aorta	Aorta
16	chr5:37035400-37071600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:37036600-37065400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:37037600-37065600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr5:37037600-37065600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr5:37037600-37067000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:37037800-37065600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:37038200-37065000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr5:37038200-37066000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:37038200-37066000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:37038200-37067200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr5:37040600-37060800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr5:37040600-37065600	Strong transcription	Fetal Intestine Large	intestine
28	chr5:37041800-37065600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr5:37042000-37065600	Strong transcription	Placenta	Placenta
30	chr5:37042200-37065600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr5:37042400-37065600	Strong transcription	Fetal Thymus	thymus
32	chr5:37042600-37063000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr5:37042800-37064000	Weak transcription	Spleen	Spleen
34	chr5:37043400-37066400	Strong transcription	Liver	Liver
35	chr5:37043600-37065200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr5:37043600-37065600	Strong transcription	Dnd41	blood
37	chr5:37043600-37065800	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr5:37043800-37060800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:37043800-37065200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:37043800-37066200	Strong transcription	Primary B cells from cord blood	blood
41	chr5:37044000-37067200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:37044200-37066600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr5:37045400-37061600	Strong transcription	HSMM	muscle
44	chr5:37049200-37061400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr5:37051000-37069200	Weak transcription	Fetal Heart	heart
46	chr5:37051200-37061400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr5:37051200-37061400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:37051200-37064000	Weak transcription	Pancreas	Pancrea
49	chr5:37051400-37060600	Weak transcription	Lung	lung
50	chr5:37052800-37058800	Weak transcription	Fetal Stomach	stomach

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