Variant report

Variant	rs2500422
Chromosome Location	chr20:25379232-25379233
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:24973762..24975336-chr20:25378149..25379762,2	MCF-7	breast:
2	chr20:25369869..25371629-chr20:25378705..25380608,2	MCF-7	breast:
3	chr20:25274830..25275740-chr20:25378372..25379283,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100997	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2474771	1.00[AMR][1000 genomes]
rs2474778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs381497	1.00[AFR][1000 genomes]
rs407925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4815430	1.00[AFR][1000 genomes]
rs496133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs574221	1.00[AFR][1000 genomes]
rs6037118	1.00[AMR][1000 genomes]
rs6050676	1.00[AFR][1000 genomes]
rs6050696	1.00[AFR][1000 genomes]
rs913792	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
9	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
11	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
12	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv482647	chr20:25308912-25481982	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
15	nsv1056997	chr20:25316663-25492339	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats 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	20 gene(s)	inside rSNPs	diseases
16	nsv1061058	chr20:25327960-25388841	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
17	nsv964440	chr20:25351740-25387631	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
18	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
19	nsv1061398	chr20:25370106-25444076	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
20	nsv1059494	chr20:25377602-25441835	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25372200-25380800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr20:25374800-25379400	Weak transcription	Hela-S3	cervix
3	chr20:25375400-25379600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr20:25377600-25379800	Enhancers	GM12878-XiMat	blood
5	chr20:25377600-25381600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:25377800-25380000	Enhancers	Fetal Intestine Large	intestine
7	chr20:25377800-25380000	Enhancers	Placenta	Placenta
8	chr20:25377800-25380200	Enhancers	Fetal Intestine Small	intestine
9	chr20:25378000-25379600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr20:25378000-25380000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr20:25378000-25380200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr20:25378000-25380400	Enhancers	A549	lung
13	chr20:25378200-25379400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr20:25378200-25379400	Weak transcription	K562	blood
15	chr20:25378200-25379600	Enhancers	HepG2	liver
16	chr20:25378200-25379800	Enhancers	Duodenum Mucosa	Duodenum
17	chr20:25378200-25379800	Enhancers	NHLF	lung
18	chr20:25378400-25379600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr20:25378400-25380000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr20:25378600-25379800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr20:25378600-25379800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr20:25378600-25379800	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr20:25378600-25379800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr20:25378600-25380000	Enhancers	Osteobl	bone
25	chr20:25378800-25379600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr20:25378800-25379800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr20:25378800-25380000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr20:25379000-25379400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr20:25379000-25379800	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr20:25379000-25380000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr20:25379000-25380000	Enhancers	Brain Anterior Caudate	brain
32	chr20:25379000-25380000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr20:25379000-25380200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr20:25379000-25380200	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr20:25379000-25380200	Enhancers	Brain Angular Gyrus	brain
36	chr20:25379000-25380200	Enhancers	NHDF-Ad	bronchial
37	chr20:25379200-25379800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr20:25379200-25379800	Enhancers	Brain Substantia Nigra	brain
39	chr20:25379200-25380000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr20:25379200-25380000	Enhancers	Brain Cingulate Gyrus	brain
41	chr20:25379200-25380200	Enhancers	Brain Hippocampus Middle	brain
42	chr20:25379200-25380200	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr20:25379200-25380200	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr20:25379200-25381000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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