Variant report

Variant	rs1183278
Chromosome Location	chr5:68739202-68739203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10035835	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10038816	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10064264	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10068576	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10077458	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10078100	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168404	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168409	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168410	0.82[ASN][1000 genomes]
rs1177556	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs182447	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2561160	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2561169	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2561172	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2561186	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28703034	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs299075	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299077	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299078	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs299088	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs299091	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs299094	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs299098	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs299099	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299102	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4252228	0.89[ASN][1000 genomes]
rs7712318	0.81[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
rs1183278	CCDC125	cis	Thyroid	GTEx
rs1183278	CCDC125	cis	lung	GTEx
rs1183278	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68712400-68740400	Weak transcription	Fetal Kidney	kidney
2	chr5:68716400-68742000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:68726200-68740000	Weak transcription	Colonic Mucosa	Colon
4	chr5:68730000-68739400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:68730400-68747400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:68730400-68747400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:68731400-68745200	Weak transcription	NHEK	skin
8	chr5:68732600-68740000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:68732600-68745200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:68732600-68745200	Weak transcription	HMEC	breast
11	chr5:68732600-68747400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr5:68732600-68750000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:68732600-68750400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:68732800-68740600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:68733600-68745800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:68734200-68739400	Weak transcription	Stomach Mucosa	stomach
17	chr5:68734200-68739800	Weak transcription	Gastric	stomach
18	chr5:68734200-68747400	Weak transcription	Lung	lung
19	chr5:68734400-68749200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr5:68736400-68740600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:68737000-68740000	Weak transcription	Pancreas	Pancrea
22	chr5:68737000-68741800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:68737000-68742000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:68737200-68739600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:68738200-68740200	Weak transcription	Liver	Liver
26	chr5:68738400-68743200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr5:68738600-68745600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:68739200-68739400	Genic enhancers	Fetal Intestine Small	intestine
29	chr5:68739200-68740200	Enhancers	HepG2	liver
30	chr5:68739200-68740400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:68739200-68742400	Enhancers	Fetal Intestine Large	intestine

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