Variant report

Variant	rs6879078
Chromosome Location	chr5:68638941-68638942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68631692..68634148-chr5:68638657..68640415,2	K562	blood:
2	chr5:68392072..68393994-chr5:68636820..68639072,2	K562	blood:
3	chr5:68637589..68639798-chr5:68660289..68662388,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10044508	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10045361	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10471350	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471774	0.80[EUR][1000 genomes]
rs10471775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471776	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940216	0.84[EUR][1000 genomes]
rs10940218	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11748974	0.84[EUR][1000 genomes]
rs12187268	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12188076	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12517724	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13178839	0.85[EUR][1000 genomes]
rs13361598	0.86[EUR][1000 genomes]
rs1530290	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2010352	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28580747	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4252228	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4473723	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4976160	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4976190	0.86[EUR][1000 genomes]
rs4976194	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58772585	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62373187	0.82[EUR][1000 genomes]
rs6450029	0.84[EUR][1000 genomes]
rs6450032	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6873869	0.84[EUR][1000 genomes]
rs6875069	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7708429	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7712318	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9291947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9291948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9791036	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6879078	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs6879078	MRPS36	cis	lymphoblastoid	seeQTL
rs6879078	CCDC125	cis	lung	GTEx

Chromatin state (count:14 , 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	chr5:68629000-68645800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:68629000-68646000	Weak transcription	Primary T cells from cord blood	blood
4	chr5:68629000-68646800	Weak transcription	NH-A	brain
5	chr5:68629200-68646000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr5:68631600-68645600	Weak transcription	Pancreas	Pancrea
7	chr5:68631600-68648600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:68632800-68645600	Weak transcription	Fetal Intestine Small	intestine
9	chr5:68636000-68648000	Weak transcription	HepG2	liver
10	chr5:68637200-68646000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:68637800-68645800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:68638000-68660200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr5:68638600-68645800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:68638800-68645800	Weak transcription	Liver	Liver

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