Variant report

Variant	rs12590397
Chromosome Location	chr14:24507823-24507824
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:24503791..24508058-chr14:24562194..24566408,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100889	Chromatin interaction
ENSG00000129535	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12588225	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12589203	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1811890	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2006084	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2277477	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277478	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2332130	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28535492	0.83[ASN][1000 genomes]
rs4981492	1.00[ASN][1000 genomes]
rs4982826	0.87[EUR][1000 genomes]
rs4982833	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3405661	chr14:24189883-24670942	Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv1217	chr14:24400565-24512689	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1049316	chr14:24405420-24583724	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv541999	chr14:24405420-24583724	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	esv2761633	chr14:24423582-24513917	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv564047	chr14:24428509-24525634	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv901497	chr14:24429249-24514449	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1052180	chr14:24429298-24555710	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv826901	chr14:24457315-24508468	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1048292	chr14:24474511-24513905	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
11	nsv1049192	chr14:24478882-24519250	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
12	nsv1037929	chr14:24478882-24522447	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
13	nsv1052857	chr14:24479375-24513905	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
14	nsv1047042	chr14:24484459-24513905	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	nsv1038839	chr14:24488131-24510197	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
16	nsv1044763	chr14:24488131-24513905	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
17	nsv1051893	chr14:24488131-24519250	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
18	nsv1043854	chr14:24488131-24522447	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
19	nsv1049849	chr14:24488384-24513905	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
20	nsv516023	chr14:24489605-24550224	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
21	nsv1038278	chr14:24494063-24513905	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
22	nsv1042507	chr14:24494153-24513905	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
23	nsv983808	chr14:24503854-24523979	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
24	nsv482170	chr14:24505710-24520580	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24506200-24520200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:24506200-24520600	Weak transcription	Spleen	Spleen
3	chr14:24506400-24508400	Enhancers	Fetal Intestine Large	intestine
4	chr14:24506400-24508400	Enhancers	Fetal Intestine Small	intestine
5	chr14:24506400-24513400	Weak transcription	NHEK	skin
6	chr14:24506800-24512000	Weak transcription	Adipose Nuclei	Adipose
7	chr14:24507000-24509600	Weak transcription	Colonic Mucosa	Colon
8	chr14:24507000-24512000	Weak transcription	Liver	Liver
9	chr14:24507200-24508600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr14:24507200-24508800	Weak transcription	Esophagus	oesophagus
11	chr14:24507200-24510400	Weak transcription	Right Ventricle	heart
12	chr14:24507200-24511800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr14:24507200-24511800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr14:24507200-24520600	Weak transcription	Lung	lung
15	chr14:24507200-24520600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr14:24507200-24520600	Weak transcription	A549	lung
17	chr14:24507400-24511600	Weak transcription	Pancreas	Pancrea
18	chr14:24507400-24511600	Weak transcription	Stomach Mucosa	stomach
19	chr14:24507600-24508400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr14:24507600-24508400	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr14:24507600-24509400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr14:24507600-24509600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr14:24507800-24508200	Enhancers	Primary neutrophils fromperipheralblood	blood

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