Variant report

Variant	rs16967035
Chromosome Location	chr15:38880178-38880179
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs56170975	0.82[ASN][1000 genomes]
rs56231408	0.84[ASN][1000 genomes]
rs60389828	0.88[ASN][1000 genomes]
rs62006162	0.88[ASN][1000 genomes]
rs62006173	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62008298	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949171	chr15:38232548-39033746	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv904085	chr15:38786114-38985513	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1046994	chr15:38806163-39239014	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv525770	chr15:38816833-39084956	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1054651	chr15:38827825-39082844	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv542358	chr15:38827825-39082844	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv904086	chr15:38829198-38931396	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16967035	ALMS1	trans	parietal	SCAN
rs16967035	CADM1	trans	lymphoblastoid	seeQTL
rs16967035	RGS11	trans	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38865600-38881000	Weak transcription	Fetal Thymus	thymus
2	chr15:38879200-38880200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:38879200-38880200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr15:38879200-38880400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr15:38879200-38880400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr15:38879200-38880600	Enhancers	Thymus	Thymus
7	chr15:38879200-38880800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr15:38879200-38881000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr15:38879400-38882200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:38879600-38880600	Enhancers	Brain Substantia Nigra	brain
11	chr15:38879600-38882000	Enhancers	Brain Cingulate Gyrus	brain
12	chr15:38879800-38880400	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr15:38879800-38880800	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr15:38879800-38881000	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr15:38880000-38880400	Enhancers	Brain Anterior Caudate	brain
16	chr15:38880000-38880400	Weak transcription	GM12878-XiMat	blood
17	chr15:38880000-38881000	Enhancers	Brain Hippocampus Middle	brain
18	chr15:38880000-38882000	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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