Variant report

Variant	rs299077
Chromosome Location	chr5:68741950-68741951
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	chr5:68740205..68742889-chr5:68789458..68791816,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10035835	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10038816	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10064264	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10068576	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10077458	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10078100	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168404	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1168409	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168410	0.81[ASN][1000 genomes]
rs1177556	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1183278	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs182447	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2561160	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2561169	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2561172	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2561186	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28371924	0.82[EUR][1000 genomes]
rs28703034	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299075	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299078	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs299088	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs299091	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299094	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs299098	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299099	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs299102	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4252228	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7712318	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs299077	CCDC125	cis	Thyroid	GTEx
rs299077	CCDC125	cis	lung	GTEx
rs299077	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68716400-68742000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:68730400-68747400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr5:68730400-68747400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:68731400-68745200	Weak transcription	NHEK	skin
5	chr5:68732600-68745200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:68732600-68745200	Weak transcription	HMEC	breast
7	chr5:68732600-68747400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:68732600-68750000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:68732600-68750400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:68733600-68745800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:68734200-68747400	Weak transcription	Lung	lung
12	chr5:68734400-68749200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr5:68737000-68742000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:68738400-68743200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:68738600-68745600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:68739200-68742400	Enhancers	Fetal Intestine Large	intestine
17	chr5:68739400-68742400	Enhancers	Fetal Intestine Small	intestine
18	chr5:68740400-68745200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:68740600-68742200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:68740600-68743000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:68740600-68745200	Weak transcription	Stomach Mucosa	stomach
22	chr5:68740600-68745400	Weak transcription	Pancreas	Pancrea
23	chr5:68740600-68746000	Weak transcription	Liver	Liver
24	chr5:68741000-68745400	Weak transcription	HepG2	liver

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