Variant report

Variant	rs4245442
Chromosome Location	chr11:71220909-71220910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000254682	Chromatin interaction
ENSG00000172890	Chromatin interaction
ENSG00000254924	Chromatin interaction
ENSG00000172893	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11234014	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2186777	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35708376	0.83[AMR][1000 genomes]
rs6592175	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7118246	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7925331	0.83[AMR][1000 genomes]
rs7926180	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7938023	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7940244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944274	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9705153	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
3	nsv468632	chr11:71200320-71289089	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv555402	chr11:71200320-71289089	Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4245442	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs4245442	RP11-660L16.2	cis	Adipose Subcutaneous	GTEx
rs4245442	RP11-660L16.2	cis	Heart Left Ventricle	GTEx
rs4245442	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4245442	RP11-660L16.2	cis	Thyroid	GTEx
rs4245442	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs4245442	RP11-660L16.2	cis	Artery Aorta	GTEx
rs4245442	RP11-660L16.2	cis	Whole Blood	GTEx
rs4245442	NADSYN1	cis	Nerve Tibial	GTEx
rs4245442	RP11-660L16.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71211800-71232400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr11:71213200-71232200	Weak transcription	Brain Angular Gyrus	brain
3	chr11:71215000-71222400	Weak transcription	HSMM	muscle
4	chr11:71215600-71236600	Weak transcription	Brain Anterior Caudate	brain
5	chr11:71216400-71235400	Weak transcription	Brain Substantia Nigra	brain
6	chr11:71217000-71222000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:71217800-71221000	Weak transcription	Liver	Liver
8	chr11:71217800-71221800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:71218400-71221000	Weak transcription	Fetal Intestine Small	intestine
10	chr11:71218400-71221200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:71220800-71222200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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

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