Variant report

Variant	rs2482938
Chromosome Location	chr20:25341317-25341318
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	chr20:25334830..25338247-chr20:25338696..25341660,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs2227891	0.82[ASN][1000 genomes]
rs2228976	0.82[ASN][1000 genomes]
rs2236180	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2258053	0.87[ASN][1000 genomes]
rs2261177	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2263205	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424701	0.87[ASN][1000 genomes]
rs2424705	0.87[ASN][1000 genomes]
rs2424707	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2482908	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2482933	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2482934	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482947	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2500395	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2500403	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2500441	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2500442	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6050603	0.87[ASN][1000 genomes]
rs6138569	0.83[EUR][1000 genomes];0.81[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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2482938	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs2482938	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs2482938	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs2482938	PYGB	cis	Whole Blood	GTEx
rs2482938	PYGB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25292600-25351600	Weak transcription	NHDF-Ad	bronchial
2	chr20:25319200-25348400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr20:25327400-25361400	Weak transcription	Primary T cells from cord blood	blood
4	chr20:25334600-25341600	Weak transcription	NHLF	lung
5	chr20:25334600-25353600	Weak transcription	Aorta	Aorta
6	chr20:25334600-25357600	Weak transcription	Fetal Muscle Leg	muscle
7	chr20:25334800-25351000	Weak transcription	Fetal Intestine Small	intestine
8	chr20:25334800-25362600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr20:25335600-25341400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr20:25335800-25341400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr20:25335800-25350200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr20:25336000-25341400	Weak transcription	Fetal Lung	lung
13	chr20:25336200-25341400	Weak transcription	Primary B cells from cord blood	blood
14	chr20:25337000-25341400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr20:25337000-25370000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr20:25337200-25341400	Weak transcription	Ovary	ovary
17	chr20:25337400-25341400	Weak transcription	A549	lung
18	chr20:25337400-25341600	Weak transcription	Fetal Stomach	stomach
19	chr20:25337400-25355600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr20:25337600-25341400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr20:25337600-25341400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr20:25337600-25341600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr20:25337600-25345400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr20:25337600-25353600	Weak transcription	Thymus	Thymus
25	chr20:25337600-25354200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr20:25337600-25362800	Weak transcription	Spleen	Spleen
27	chr20:25337800-25341400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr20:25337800-25341400	Weak transcription	Colonic Mucosa	Colon
29	chr20:25337800-25341600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr20:25337800-25345000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr20:25337800-25350400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr20:25338000-25344000	Weak transcription	Fetal Brain Female	brain
33	chr20:25338000-25345000	Weak transcription	Left Ventricle	heart
34	chr20:25338000-25348000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr20:25338000-25369400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr20:25338200-25341600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr20:25338200-25345400	Weak transcription	Right Ventricle	heart
38	chr20:25338200-25350000	Weak transcription	Brain Angular Gyrus	brain
39	chr20:25338200-25359000	Weak transcription	Fetal Intestine Large	intestine
40	chr20:25338600-25344600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr20:25338600-25345000	Weak transcription	Gastric	stomach
42	chr20:25339200-25341600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr20:25339200-25341600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr20:25339200-25344800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr20:25339400-25341600	Weak transcription	Fetal Heart	heart
46	chr20:25339400-25341800	Weak transcription	Brain Anterior Caudate	brain
47	chr20:25339400-25341800	Weak transcription	Brain Hippocampus Middle	brain
48	chr20:25339400-25344600	Weak transcription	Esophagus	oesophagus
49	chr20:25339400-25345000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr20:25339400-25345000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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