Variant report

Variant	rs2290990
Chromosome Location	chr5:111497330-111497331
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:110427038..110429477-chr5:111496823..111498609,2	K562	blood:
2	chr5:111495904..111497786-chr5:111539852..111541904,2	K562	blood:
3	chr5:110427977..110430088-chr5:111495107..111498582,4	K562	blood:
4	chr5:111092933..111095338-chr5:111496527..111499231,3	MCF-7	breast:
5	chr5:111496508..111497358-chr6:31795058..31795974,2	NB4	blood:
6	chr5:111495302..111497808-chr5:111754204..111756858,3	MCF-7	breast:
7	chr5:110848137..110849903-chr5:111495270..111497479,2	MCF-7	breast:
8	chr5:110846086..110848469-chr5:111495331..111498521,3	K562	blood:
9	chr5:111496976..111498708-chr5:111754134..111756098,2	MCF-7	breast:
10	chr5:110847947..110849920-chr5:111495605..111497967,3	K562	blood:
11	chr5:111496112..111498947-chr5:112256676..112259616,2	K562	blood:
12	chr5:111100842..111103505-chr5:111497212..111499866,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000134986	Chromatin interaction
ENSG00000246859	Chromatin interaction
ENSG00000268358	Chromatin interaction
ENSG00000164211	Chromatin interaction
ENSG00000129625	Chromatin interaction
ENSG00000134987	Chromatin interaction
ENSG00000251187	Chromatin interaction
ENSG00000129595	Chromatin interaction
ENSG00000204388	Chromatin interaction
ENSG00000253613	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10045569	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1078129	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs13165611	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs17134155	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs17134162	0.86[ASN][1000 genomes]
rs17134228	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs17134250	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs17265886	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs1863960	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs2162733	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs2303657	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs2900059	0.89[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2900060	0.91[EUR][1000 genomes]
rs3797320	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs3816657	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55812441	0.91[EUR][1000 genomes]
rs56158171	0.97[EUR][1000 genomes]
rs61482608	0.97[EUR][1000 genomes]
rs6873159	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs73787781	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7449256	0.97[EUR][1000 genomes]
rs7700705	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7711555	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7713216	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7720064	0.90[CEU][hapmap];0.97[EUR][1000 genomes]
rs7720344	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7730625	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[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	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111496000-111497400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr5:111496000-111497400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:111496000-111497400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:111496000-111497400	Active TSS	Fetal Brain Female	brain
5	chr5:111496000-111497400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr5:111496000-111497400	Active TSS	HSMM	muscle
7	chr5:111496000-111497600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:111496000-111497800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:111496000-111497800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:111496000-111497800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:111496000-111497800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:111496000-111497800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:111496000-111497800	Active TSS	Ovary	ovary
14	chr5:111496000-111497800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr5:111496000-111497800	Active TSS	NHLF	lung
16	chr5:111496200-111497600	Active TSS	Fetal Intestine Small	intestine
17	chr5:111496200-111497800	Active TSS	H9 Cell Line	embryonic stem cell
18	chr5:111496200-111497800	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr5:111496200-111497800	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr5:111496200-111497800	Active TSS	Fetal Heart	heart
21	chr5:111496200-111498000	Active TSS	H1 Cell Line	embryonic stem cell
22	chr5:111496200-111498200	Active TSS	Psoas Muscle	Psoas
23	chr5:111496200-111498200	Active TSS	Right Atrium	heart
24	chr5:111496400-111497400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:111496400-111497400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr5:111496400-111497400	Active TSS	Stomach Mucosa	stomach
27	chr5:111496400-111497400	Active TSS	Spleen	Spleen
28	chr5:111496400-111497400	Active TSS	GM12878-XiMat	blood
29	chr5:111496400-111497400	Active TSS	NH-A	brain
30	chr5:111496400-111497600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:111496400-111497600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:111496400-111497600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:111496400-111497600	Active TSS	Aorta	Aorta
34	chr5:111496400-111497600	Active TSS	Esophagus	oesophagus
35	chr5:111496400-111497600	Active TSS	Gastric	stomach
36	chr5:111496400-111497600	Active TSS	Left Ventricle	heart
37	chr5:111496400-111497600	Active TSS	Lung	lung
38	chr5:111496400-111497600	Active TSS	Pancreas	Pancrea
39	chr5:111496400-111497800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr5:111496400-111497800	Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr5:111496400-111497800	Active TSS	Fetal Muscle Trunk	muscle
42	chr5:111496400-111497800	Active TSS	Hela-S3	cervix
43	chr5:111496400-111497800	Active TSS	HMEC	breast
44	chr5:111496400-111497800	Active TSS	NHDF-Ad	bronchial
45	chr5:111496400-111498000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:111496400-111498000	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr5:111496400-111498000	Active TSS	Muscle Satellite Cultured Cells	--
48	chr5:111496400-111498000	Active TSS	Fetal Intestine Large	intestine
49	chr5:111496400-111498200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:111496400-111498600	Active TSS	Right Ventricle	heart

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