Variant report

Variant	rs7647661
Chromosome Location	chr3:70118356-70118357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MITF-5	chr3:70117349-70119600	NONHSAT090375

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1027233	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1027234	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1157456	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923682	0.84[AMR][1000 genomes]
rs11926368	0.84[AMR][1000 genomes]
rs12495230	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1388649	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1491686	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1491695	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1491698	0.84[AMR][1000 genomes]
rs1492055	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1492056	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1546075	0.84[AMR][1000 genomes]
rs1873583	0.83[AMR][1000 genomes]
rs1873584	0.84[AMR][1000 genomes]
rs2131122	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28524674	0.84[AMR][1000 genomes]
rs6549261	0.84[AMR][1000 genomes]
rs6549262	0.84[AMR][1000 genomes]
rs6549264	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6549265	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6549266	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6549267	0.84[AFR][1000 genomes]
rs6772684	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6784666	0.81[AMR][1000 genomes]
rs6809508	0.84[AMR][1000 genomes]
rs7634340	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7634564	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7651972	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9310178	0.84[AMR][1000 genomes]
rs9310179	0.84[AMR][1000 genomes]
rs9310180	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs956436	0.84[AMR][1000 genomes]
rs9809122	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9815287	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9834141	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9839734	0.84[AMR][1000 genomes]
rs9840397	0.84[AMR][1000 genomes]
rs9840590	0.84[AMR][1000 genomes]
rs9840951	0.80[AFR][1000 genomes]
rs9849031	0.84[AMR][1000 genomes]
rs9851891	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9863457	0.84[AMR][1000 genomes]
rs9868203	0.84[AMR][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	nsv533396	chr3:69964029-70538306	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7647661	RP11-460N16.1	cis	Artery Aorta	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:70107400-70120400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:70107600-70120200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:70112600-70120600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:70113800-70119800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:70113800-70120200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:70113800-70120400	Weak transcription	Brain Anterior Caudate	brain
7	chr3:70113800-70120400	Weak transcription	Brain Substantia Nigra	brain
8	chr3:70113800-70123800	Weak transcription	Gastric	stomach
9	chr3:70115000-70120200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:70115000-70120200	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:70117200-70118600	Enhancers	Fetal Heart	heart
12	chr3:70117200-70121200	Weak transcription	Psoas Muscle	Psoas
13	chr3:70117600-70118800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:70117600-70119800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:70117800-70118600	Weak transcription	Aorta	Aorta
16	chr3:70118200-70120800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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