Variant report

Variant	rs299090
Chromosome Location	chr5:68716463-68716464
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	chr5:68714328..68717643-chr5:68787118..68789259,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197822	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10035835	0.81[EUR][1000 genomes]
rs10036674	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10037276	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10060524	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10072904	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10077413	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10078100	0.80[EUR][1000 genomes]
rs1168402	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168403	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1168405	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168406	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168407	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168408	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168409	0.80[EUR][1000 genomes]
rs1168411	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1177556	0.81[EUR][1000 genomes]
rs1177557	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1183879	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1185246	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs182447	0.86[EUR][1000 genomes]
rs2434507	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2439720	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2439722	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2561159	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2561160	0.85[EUR][1000 genomes]
rs2561171	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2561182	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2561183	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2561186	0.80[EUR][1000 genomes]
rs2583699	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2583701	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28371924	0.83[EUR][1000 genomes]
rs28570129	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299072	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299073	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299074	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299075	0.81[EUR][1000 genomes]
rs299076	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299078	0.84[EUR][1000 genomes]
rs299079	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299080	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299081	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299082	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299083	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299084	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299085	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs299086	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299087	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299088	0.81[EUR][1000 genomes]
rs299091	0.81[EUR][1000 genomes]
rs299092	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299093	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs299094	0.81[EUR][1000 genomes]
rs299095	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs299096	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299097	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs299098	0.81[EUR][1000 genomes]
rs299099	0.81[EUR][1000 genomes]
rs299101	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299102	0.81[EUR][1000 genomes]
rs3797091	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55747363	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62371717	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6450038	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7447816	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7448722	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7730350	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7731269	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9686715	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs299090	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs299090	CCDC125	cis	lung	GTEx
rs299090	MRPS36	cis	lymphoblastoid	seeQTL
rs299090	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68697800-68717000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr5:68711400-68718200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:68711600-68717200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:68711600-68717400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:68711600-68722800	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:68711600-68724000	Weak transcription	Right Atrium	heart
7	chr5:68711800-68717200	Weak transcription	Osteobl	bone
8	chr5:68711800-68723600	Weak transcription	Small Intestine	intestine
9	chr5:68711800-68725000	Weak transcription	Fetal Muscle Leg	muscle
10	chr5:68711800-68731000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:68712000-68718800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:68712400-68717200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:68712400-68719200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr5:68712400-68719400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr5:68712400-68731000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:68712400-68735600	Weak transcription	Hela-S3	cervix
17	chr5:68712400-68739000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:68712400-68740400	Weak transcription	Fetal Kidney	kidney
19	chr5:68712600-68718400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:68712800-68738200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr5:68713000-68718800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:68714400-68723800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:68714800-68716600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:68714800-68717400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr5:68715000-68717400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:68715200-68716600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr5:68715600-68716800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr5:68715800-68716600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr5:68715800-68717400	Weak transcription	NHLF	lung
30	chr5:68716000-68716800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:68716000-68717400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:68716000-68717400	Weak transcription	Fetal Intestine Small	intestine
33	chr5:68716000-68717600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:68716000-68718800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:68716000-68719000	Weak transcription	Fetal Intestine Large	intestine
36	chr5:68716000-68728800	Weak transcription	Lung	lung
37	chr5:68716000-68732200	Weak transcription	Esophagus	oesophagus
38	chr5:68716000-68733600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr5:68716000-68735800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr5:68716000-68738200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr5:68716000-68738800	Weak transcription	Fetal Stomach	stomach
42	chr5:68716200-68718600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr5:68716200-68718800	Weak transcription	Pancreas	Pancrea
44	chr5:68716200-68719000	Weak transcription	Gastric	stomach
45	chr5:68716200-68724800	Weak transcription	Stomach Mucosa	stomach
46	chr5:68716200-68728200	Weak transcription	Liver	Liver
47	chr5:68716200-68728400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr5:68716200-68728400	Weak transcription	Placenta	Placenta
49	chr5:68716200-68738000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr5:68716400-68716800	Active TSS	Duodenum Mucosa	Duodenum

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