Variant report

Variant	rs1541518
Chromosome Location	chr7:31148279-31148280
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1008385	0.85[EUR][1000 genomes]
rs1159040	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2284224	0.88[ASW][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2284225	0.88[ASW][hapmap];0.82[CEU][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2299908	0.80[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2302476	0.82[EUR][1000 genomes]
rs4472421	0.89[AFR][1000 genomes]
rs4723045	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4723046	0.81[CEU][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4723047	0.81[ASW][hapmap];0.82[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58094779	0.85[EUR][1000 genomes]
rs6954589	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs741057	0.87[CEU][hapmap];0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7786849	0.84[AFR][1000 genomes]
rs7793414	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1016256	chr7:30649212-31163056	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1023120	chr7:30655070-31185096	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv2761316	chr7:30655082-31166676	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv527038	chr7:30657467-31161945	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv916877	chr7:30661135-31154731	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1017168	chr7:30663213-31166676	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv1017808	chr7:30671936-31150473	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv915784	chr7:31134685-31870517	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1541518	RP9P	cis	cerebellum	SCAN
rs1541518	AVL9	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:31117400-31162000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:31133200-31154600	Weak transcription	Brain Angular Gyrus	brain
3	chr7:31133400-31154200	Weak transcription	Fetal Brain Male	brain
4	chr7:31136600-31149600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr7:31138400-31148800	Strong transcription	Fetal Brain Female	brain
6	chr7:31142400-31149400	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:31143400-31148600	Strong transcription	Fetal Stomach	stomach
8	chr7:31144600-31156400	Weak transcription	Right Atrium	heart
9	chr7:31146600-31151000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr7:31147600-31150200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr7:31147600-31150600	Weak transcription	Brain Germinal Matrix	brain
12	chr7:31147600-31150800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:31147600-31156600	Weak transcription	Fetal Muscle Leg	muscle
14	chr7:31147800-31148600	Enhancers	Spleen	Spleen
15	chr7:31148000-31154400	Weak transcription	Fetal Muscle Trunk	muscle

Quick Search:

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

what's new

Quick links