Variant report

Variant	rs6875069
Chromosome Location	chr5:68631546-68631547
allele	A/G
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	FOS	chr5:68631450-68631706	MCF10A-Er-Src	breast:	n/a	chr5:68631612-68631622 chr5:68631613-68631621 chr5:68631612-68631622 chr5:68631612-68631622 chr5:68631612-68631622
2	MYC	chr5:68631518-68631665	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr5:68631400-68631550	HRPEpiC	eye:	n/a	n/a
4	FOS	chr5:68631537-68631731	MCF10A-Er-Src	breast:	n/a	chr5:68631612-68631622 chr5:68631613-68631621 chr5:68631612-68631622 chr5:68631612-68631622 chr5:68631612-68631622
5	FOS	chr5:68631519-68631732	MCF10A-Er-Src	breast:	n/a	chr5:68631612-68631622 chr5:68631613-68631621 chr5:68631612-68631622 chr5:68631612-68631622 chr5:68631612-68631622

No.	Distal block	Cell Line	Cell type
1	chr5:68626792..68633026-chr5:68660168..68667090,13	MCF-7	breast:
2	chr5:68626462..68633259-chr5:68656360..68665608,14	MCF-7	breast:
3	chr5:68625780..68629489-chr5:68629805..68632060,4	MCF-7	breast:
4	chr5:68338368..68339599-chr5:68630334..68631582,4	K562	blood:
5	chr5:68513358..68515252-chr5:68629266..68631706,2	K562	blood:
6	chr5:68630799..68633457-chr5:68666139..68668390,2	K562	blood:

Variant related genes	Relation type
CCDC125	TF binding region
ENSG00000085231	Chromatin interaction
ENSG00000134056	Chromatin interaction
ENSG00000183323	Chromatin interaction
ENSG00000152942	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10044508	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10045361	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10471350	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10471774	0.81[EUR][1000 genomes]
rs10471775	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10471776	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10940216	0.85[EUR][1000 genomes]
rs10940218	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11748974	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12187268	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12188076	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12517724	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13178839	0.84[EUR][1000 genomes]
rs13361598	0.85[EUR][1000 genomes]
rs1530290	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2010352	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28580747	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4252228	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4473723	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4976160	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4976190	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4976194	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58772585	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62373187	0.83[EUR][1000 genomes]
rs6450029	0.85[EUR][1000 genomes]
rs6450032	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6873869	0.85[EUR][1000 genomes]
rs6879078	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7708429	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7712318	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9291947	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9291948	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9791036	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv969960	chr5:68613678-68646127	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3515528	chr5:68624487-68653938	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3515529	chr5:68624487-68653938	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	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
7	nsv968922	chr5:68628679-68631659	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6875069	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs6875069	CCDC125	cis	lung	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68628800-68649200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:68629000-68631800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:68629000-68645800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:68629000-68646000	Weak transcription	Primary T cells from cord blood	blood
5	chr5:68629000-68646800	Weak transcription	NH-A	brain
6	chr5:68629200-68646000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr5:68630000-68632200	Weak transcription	Right Atrium	heart
8	chr5:68630400-68631600	Enhancers	NHEK	skin
9	chr5:68630400-68631800	Enhancers	Hela-S3	cervix
10	chr5:68630800-68631600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr5:68630800-68631600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:68630800-68631800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr5:68630800-68631800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr5:68630800-68632200	Enhancers	K562	blood
15	chr5:68630800-68632600	Enhancers	Fetal Intestine Large	intestine
16	chr5:68631000-68631600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:68631000-68632200	Enhancers	HepG2	liver
18	chr5:68631000-68632800	Enhancers	Fetal Intestine Small	intestine
19	chr5:68631200-68631600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:68631200-68631600	Enhancers	HMEC	breast
21	chr5:68631200-68631800	Weak transcription	Fetal Muscle Leg	muscle
22	chr5:68631400-68631600	Enhancers	Pancreas	Pancrea

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