Variant report

Variant	rs2561182
Chromosome Location	chr5:68733645-68733646
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68732288..68733823-chr5:68786804..68789445,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197822	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10036674	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10037276	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10060524	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10072904	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10077413	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168402	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168403	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1168405	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168406	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168407	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168408	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168411	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1177557	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1183879	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1185246	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs182447	0.86[EUR][1000 genomes]
rs2434507	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439720	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439721	0.82[ASN][1000 genomes]
rs2439722	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2561159	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2561160	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2561171	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2561183	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583699	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2583701	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28371924	0.85[EUR][1000 genomes]
rs28570129	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299072	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299073	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299074	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299076	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299078	0.85[EUR][1000 genomes]
rs299079	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299080	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299081	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299082	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299083	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299084	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299085	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs299086	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299087	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299090	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs299092	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs299093	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299095	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299096	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs299097	0.86[EUR][1000 genomes]
rs299101	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3797091	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55747363	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62371717	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450038	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7447816	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7448722	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7730350	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731269	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9686715	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1018410	chr5:68692244-68822384	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv969961	chr5:68728421-68738498	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2561182	CCDC125	cis	lung	GTEx
rs2561182	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs2561182	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68712400-68735600	Weak transcription	Hela-S3	cervix
2	chr5:68712400-68739000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:68712400-68740400	Weak transcription	Fetal Kidney	kidney
4	chr5:68712800-68738200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:68716000-68735800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr5:68716000-68738200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:68716000-68738800	Weak transcription	Fetal Stomach	stomach
8	chr5:68716200-68738000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:68716400-68742000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:68725400-68735800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:68726200-68740000	Weak transcription	Colonic Mucosa	Colon
12	chr5:68727400-68734200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:68728200-68734200	Strong transcription	Liver	Liver
14	chr5:68728800-68734200	Strong transcription	Lung	lung
15	chr5:68729000-68738200	Weak transcription	GM12878-XiMat	blood
16	chr5:68730000-68739400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:68730200-68734400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:68730400-68747400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr5:68730400-68747400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:68731400-68733800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:68731400-68745200	Weak transcription	NHEK	skin
22	chr5:68731800-68734000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:68731800-68736400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:68732600-68733800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:68732600-68733800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:68732600-68740000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr5:68732600-68745200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr5:68732600-68745200	Weak transcription	HMEC	breast
29	chr5:68732600-68747400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr5:68732600-68750000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr5:68732600-68750400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr5:68732800-68736600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:68732800-68740600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:68733000-68734400	Genic enhancers	Fetal Intestine Small	intestine
35	chr5:68733000-68738600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:68733200-68734400	Enhancers	Fetal Intestine Large	intestine
37	chr5:68733400-68734200	Enhancers	Pancreas	Pancrea
38	chr5:68733400-68734200	Enhancers	Stomach Mucosa	stomach
39	chr5:68733600-68734200	Enhancers	Gastric	stomach
40	chr5:68733600-68734400	Enhancers	Duodenum Mucosa	Duodenum
41	chr5:68733600-68734400	Enhancers	HepG2	liver
42	chr5:68733600-68745800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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