Variant report

Variant	rs16971175
Chromosome Location	chr15:33748434-33748435
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12050634	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12439831	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12440037	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16971225	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2676093	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs34916404	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4356445	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59918853	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60860756	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8043019	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533346	chr15:33469439-33809641	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv832964	chr15:33608771-33784018	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv1043046	chr15:33714908-34321330	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv34041	chr15:33720726-33871487	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	esv34037	chr15:33732616-34049083	Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16971175	RYR3	cis	Muscle Skeletal	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33741600-33765400	Weak transcription	Fetal Muscle Leg	muscle
2	chr15:33742200-33748800	Weak transcription	Esophagus	oesophagus
3	chr15:33744400-33750400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:33744400-33750400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:33744600-33750400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:33745800-33748600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr15:33747000-33748800	Weak transcription	Brain Anterior Caudate	brain
8	chr15:33747200-33748600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:33747600-33750400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:33747600-33752200	Weak transcription	Fetal Kidney	kidney
11	chr15:33748400-33748800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:33748400-33749000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr15:33748400-33749000	Enhancers	Cortex derived primary cultured neurospheres	brain

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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