Variant report

Variant	rs73111297
Chromosome Location	chr20:25560209-25560210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25559789..25563161-chr20:25564263..25567245,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101004	Chromatin interaction

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

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

rs_ID	r²[population]
rs110302	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs242121	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242126	0.81[EUR][1000 genomes]
rs242127	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242128	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs400630	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403424	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037138	0.86[AFR][1000 genomes]
rs6037154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050672	0.86[AFR][1000 genomes]
rs6050691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050694	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6138635	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73111300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73113113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS 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
5	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv912832	chr20:25527984-25595175	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv912833	chr20:25539486-25595175	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25521600-25565000	Weak transcription	Aorta	Aorta
2	chr20:25524400-25565000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr20:25532600-25565000	Weak transcription	HSMMtube	muscle
4	chr20:25534800-25561400	Weak transcription	Right Atrium	heart
5	chr20:25535000-25561400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr20:25535800-25565000	Weak transcription	Fetal Kidney	kidney
7	chr20:25544600-25565000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr20:25546400-25565000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr20:25548800-25565200	Weak transcription	Esophagus	oesophagus
10	chr20:25550600-25561200	Weak transcription	Gastric	stomach
11	chr20:25552000-25565000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr20:25552200-25564800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr20:25555200-25561200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr20:25555200-25564800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr20:25555200-25565000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr20:25555200-25565000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr20:25555400-25561200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr20:25555400-25565000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr20:25555400-25565000	Weak transcription	Brain Anterior Caudate	brain
20	chr20:25555400-25565000	Weak transcription	NHLF	lung
21	chr20:25557000-25565000	Weak transcription	Thymus	Thymus
22	chr20:25558200-25561400	Weak transcription	Pancreas	Pancrea
23	chr20:25558200-25565200	Weak transcription	Spleen	Spleen
24	chr20:25558800-25561200	Strong transcription	Fetal Brain Female	brain
25	chr20:25559000-25562000	Enhancers	Fetal Heart	heart
26	chr20:25559400-25560600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr20:25559400-25560800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr20:25559600-25560400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr20:25559600-25560400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr20:25559600-25560400	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr20:25559600-25560400	Enhancers	Muscle Satellite Cultured Cells	--
32	chr20:25559600-25560400	Genic enhancers	Fetal Intestine Small	intestine
33	chr20:25559600-25560400	Flanking Active TSS	HepG2	liver
34	chr20:25559600-25560400	Enhancers	NH-A	brain
35	chr20:25559600-25560600	Enhancers	H1 Cell Line	embryonic stem cell
36	chr20:25559600-25560600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr20:25559600-25560600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr20:25559600-25560600	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr20:25559600-25560600	Genic enhancers	Fetal Muscle Trunk	muscle
40	chr20:25559600-25561000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr20:25559600-25561200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr20:25559600-25561400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr20:25559600-25561800	Genic enhancers	A549	lung
44	chr20:25559800-25560400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr20:25559800-25560400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr20:25559800-25560400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr20:25559800-25560400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr20:25559800-25560400	Genic enhancers	Fetal Stomach	stomach
49	chr20:25559800-25560400	Enhancers	Lung	lung
50	chr20:25559800-25560400	Enhancers	Ovary	ovary

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