Variant report

Variant	rs55792313
Chromosome Location	chr20:25521255-25521256
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25521002..25521665-chr20:25650642..25651281,2	MCF-7	breast:
2	chr20:25476419..25480130-chr20:25519164..25522649,4	MCF-7	breast:
3	chr20:25518724..25523016-chr20:25601749..25604904,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170191	Chromatin interaction
ENSG00000236542	Chromatin interaction
ENSG00000101004	Chromatin interaction
ENSG00000213742	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11698953	0.82[ASN][1000 genomes]
rs11698992	0.85[ASN][1000 genomes]
rs11699872	1.00[ASN][1000 genomes]
rs11700213	0.83[ASN][1000 genomes]
rs11700297	0.82[ASN][1000 genomes]
rs11700338	0.82[ASN][1000 genomes]
rs12480853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481037	0.82[ASN][1000 genomes]
rs12625991	0.85[ASN][1000 genomes]
rs1888037	0.88[ASN][1000 genomes]
rs56238023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57803591	0.80[ASN][1000 genomes]
rs6107050	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6115202	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6115227	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73109499	0.86[ASN][1000 genomes]
rs73597820	0.84[ASN][1000 genomes]
rs73597824	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9305141	0.83[EUR][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	nsv1062765	chr20:25466482-25556751	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv544225	chr20:25466482-25556751	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55792313	PYGB	cis	Skin Sun Exposed Lower leg	GTEx
rs55792313	ABHD12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:25514400-25522400	Weak transcription	NH-A	brain
3	chr20:25517800-25554600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr20:25518800-25524400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr20:25518800-25530200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:25519000-25521800	Weak transcription	Thymus	Thymus
7	chr20:25519000-25522600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr20:25519200-25521400	Enhancers	Pancreas	Pancrea
9	chr20:25519400-25521400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr20:25519400-25521400	Enhancers	Fetal Heart	heart
11	chr20:25519400-25524000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr20:25519600-25521400	Enhancers	Fetal Muscle Trunk	muscle
13	chr20:25519600-25521400	Genic enhancers	Fetal Stomach	stomach
14	chr20:25519600-25521600	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr20:25519600-25522000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr20:25519600-25523000	Enhancers	Fetal Intestine Large	intestine
17	chr20:25519800-25521400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr20:25519800-25521400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr20:25519800-25521400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr20:25519800-25521600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr20:25519800-25521600	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr20:25519800-25521800	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr20:25519800-25523000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr20:25519800-25523000	Enhancers	Fetal Thymus	thymus
25	chr20:25520000-25521400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr20:25520000-25521400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr20:25520000-25521400	Active TSS	Colon Smooth Muscle	Colon
28	chr20:25520000-25521600	Active TSS	Colonic Mucosa	Colon
29	chr20:25520000-25521600	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr20:25520000-25522000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr20:25520000-25532000	Weak transcription	Dnd41	blood
32	chr20:25520200-25521400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr20:25520200-25521400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr20:25520200-25521400	Active TSS	Brain Anterior Caudate	brain
35	chr20:25520200-25521400	Active TSS	Rectal Smooth Muscle	rectum
36	chr20:25520200-25521400	Flanking Active TSS	Osteobl	bone
37	chr20:25520200-25521600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr20:25520200-25521600	Active TSS	Brain Cingulate Gyrus	brain
39	chr20:25520200-25522200	Enhancers	Fetal Brain Male	brain
40	chr20:25520200-25529000	Weak transcription	Stomach Mucosa	stomach
41	chr20:25520400-25521400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr20:25520400-25521400	Active TSS	Brain Angular Gyrus	brain
43	chr20:25520400-25521400	Active TSS	Brain Hippocampus Middle	brain
44	chr20:25520400-25521400	Active TSS	Brain Substantia Nigra	brain
45	chr20:25520400-25521400	Active TSS	Esophagus	oesophagus
46	chr20:25520400-25521400	Active TSS	Right Atrium	heart
47	chr20:25520400-25521400	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr20:25520400-25521600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr20:25520400-25521600	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr20:25520400-25521600	Active TSS	Rectal Mucosa Donor 31	rectum

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