Variant report

Variant	rs299087
Chromosome Location	chr5:68712772-68712773
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:68712291-68713236	K562	blood:	n/a	n/a
2	POLR2A	chr5:68710641-68713455	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:68712271..68714793-chr7:7679143..7681371,2	MCF-7	breast:
2	chr5:68711082..68712894-chr5:68825364..68828331,2	MCF-7	breast:
3	chr5:68709515..68715463-chr5:68785927..68791978,14	MCF-7	breast:
4	chr5:68708231..68714128-chr5:68786986..68792913,14	MCF-7	breast:

Variant related genes	Relation type
MARVELD2	TF binding region
ENSG00000106399	Chromatin interaction
ENSG00000197822	Chromatin interaction
ENSG00000219545	Chromatin interaction
ENSG00000212260	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10035835	0.81[EUR][1000 genomes]
rs10036674	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10037276	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10060524	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10072904	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077413	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10078100	0.80[EUR][1000 genomes]
rs1168402	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168403	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168405	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168406	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168407	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168408	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168409	0.80[EUR][1000 genomes]
rs1168411	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1177556	0.81[EUR][1000 genomes]
rs1177557	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1183879	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1185246	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182447	0.86[EUR][1000 genomes]
rs2434507	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2439720	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439722	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2561159	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2561160	0.85[EUR][1000 genomes]
rs2561171	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2561182	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2561183	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2561186	0.80[EUR][1000 genomes]
rs2583699	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2583701	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28371924	0.83[EUR][1000 genomes]
rs28570129	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299072	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299073	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299074	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs299075	0.81[EUR][1000 genomes]
rs299076	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299078	0.84[EUR][1000 genomes]
rs299079	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299080	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299081	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299082	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299083	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299084	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299085	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs299086	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299088	0.81[EUR][1000 genomes]
rs299090	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299091	0.81[EUR][1000 genomes]
rs299092	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299093	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299094	0.81[EUR][1000 genomes]
rs299095	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299096	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs299097	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs299098	0.81[EUR][1000 genomes]
rs299099	0.81[EUR][1000 genomes]
rs299101	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299102	0.81[EUR][1000 genomes]
rs3797091	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55747363	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62371717	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6450038	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7447816	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7448722	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7730350	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7731269	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686715	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs299087	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs299087	MRPS36	cis	lymphoblastoid	seeQTL
rs299087	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68668000-68713000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:68697800-68717000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:68701200-68713800	Weak transcription	K562	blood
4	chr5:68707800-68712800	Weak transcription	HSMMtube	muscle
5	chr5:68710600-68712800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr5:68710600-68712800	Active TSS	Fetal Intestine Small	intestine
7	chr5:68710600-68712800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr5:68710600-68713200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:68710800-68712800	Active TSS	Fetal Intestine Large	intestine
10	chr5:68710800-68712800	Active TSS	Pancreas	Pancrea
11	chr5:68710800-68712800	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr5:68711000-68712800	Active TSS	Stomach Mucosa	stomach
13	chr5:68711000-68713800	Weak transcription	HSMM	muscle
14	chr5:68711400-68713000	Weak transcription	Psoas Muscle	Psoas
15	chr5:68711400-68716200	Weak transcription	Aorta	Aorta
16	chr5:68711400-68718200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:68711600-68715200	Weak transcription	NHLF	lung
18	chr5:68711600-68715400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:68711600-68715600	Weak transcription	Spleen	Spleen
20	chr5:68711600-68717200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:68711600-68717400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:68711600-68722800	Weak transcription	Brain Hippocampus Middle	brain
23	chr5:68711600-68724000	Weak transcription	Right Atrium	heart
24	chr5:68711800-68713400	Weak transcription	Dnd41	blood
25	chr5:68711800-68715200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:68711800-68715200	Weak transcription	Lung	lung
27	chr5:68711800-68717200	Weak transcription	Osteobl	bone
28	chr5:68711800-68723600	Weak transcription	Small Intestine	intestine
29	chr5:68711800-68725000	Weak transcription	Fetal Muscle Leg	muscle
30	chr5:68711800-68731000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:68712000-68713000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:68712000-68713000	Flanking Active TSS	NHEK	skin
33	chr5:68712000-68713600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr5:68712000-68715600	Weak transcription	Primary T cells from cord blood	blood
35	chr5:68712000-68718800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:68712400-68713000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:68712400-68713000	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr5:68712400-68713200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr5:68712400-68713200	Enhancers	HepG2	liver
40	chr5:68712400-68714800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:68712400-68714800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:68712400-68715200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr5:68712400-68715200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr5:68712400-68715200	Weak transcription	Esophagus	oesophagus
45	chr5:68712400-68715200	Weak transcription	Placenta	Placenta
46	chr5:68712400-68715200	Weak transcription	Fetal Stomach	stomach
47	chr5:68712400-68715200	Weak transcription	Gastric	stomach
48	chr5:68712400-68715600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr5:68712400-68715600	Weak transcription	Fetal Lung	lung
50	chr5:68712400-68715600	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links