Variant report

Variant	rs2239499
Chromosome Location	chr3:42567002-42567003
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	POLR2A	chr3:42564995-42567233	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42566788..42568912-chr3:42571807..42573949,2	K562	blood:

Variant related genes	Relation type
VIPR1	TF binding region
ENSG00000232354	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2239500	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267534	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267535	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2267536	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2267537	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267538	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284132	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28684623	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs450812	0.87[EUR][1000 genomes]
rs58526597	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs735773	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7625494	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7635291	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7640893	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs811198	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9841214	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][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	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42547600-42579000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:42552200-42581000	Weak transcription	Pancreas	Pancrea
3	chr3:42552400-42570000	Weak transcription	Fetal Stomach	stomach
4	chr3:42557600-42569800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:42557600-42571600	Weak transcription	Brain Angular Gyrus	brain
6	chr3:42557600-42574000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:42557600-42574400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:42557800-42586000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:42557800-42590400	Weak transcription	Aorta	Aorta
10	chr3:42558000-42570200	Weak transcription	Adipose Nuclei	Adipose
11	chr3:42558000-42573000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:42558000-42585200	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:42560200-42573400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:42561000-42581000	Weak transcription	Gastric	stomach
15	chr3:42561400-42570400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr3:42561800-42568600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:42562000-42567600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:42562400-42567600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:42562400-42570800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:42562400-42586800	Weak transcription	Small Intestine	intestine
21	chr3:42562800-42567200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:42562800-42574200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:42563000-42572400	Weak transcription	Right Ventricle	heart
24	chr3:42563600-42575000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr3:42564000-42577400	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr3:42564400-42570600	Genic enhancers	Lung	lung
27	chr3:42565000-42567200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:42565200-42576400	Enhancers	Spleen	Spleen
29	chr3:42565600-42567200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:42565600-42567800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr3:42565600-42570400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:42565800-42567400	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr3:42565800-42568200	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr3:42565800-42570000	Strong transcription	Colonic Mucosa	Colon
35	chr3:42566000-42571800	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:42566200-42567400	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr3:42566200-42571200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:42566200-42571400	Enhancers	Fetal Thymus	thymus
39	chr3:42566400-42567400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:42566400-42567600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:42566400-42567600	Genic enhancers	Fetal Intestine Small	intestine
42	chr3:42566400-42567800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:42566400-42568400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr3:42566400-42571000	Enhancers	Primary T cells fromperipheralblood	blood
45	chr3:42566600-42567200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:42566600-42567200	Enhancers	Esophagus	oesophagus
47	chr3:42566600-42567400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:42566600-42567600	Enhancers	Primary B cells from cord blood	blood
49	chr3:42566600-42567800	Genic enhancers	Fetal Intestine Large	intestine
50	chr3:42566600-42568200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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