Variant report

Variant	rs1028018
Chromosome Location	chr9:8659757-8659758
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10758985	0.85[CHD][hapmap];0.89[GIH][hapmap]
rs10815923	0.82[CEU][hapmap]
rs1415722	0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1415724	0.87[JPT][hapmap]
rs16928221	0.87[JPT][hapmap]
rs72700331	0.81[AFR][1000 genomes]
rs7851001	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs7859849	0.82[CEU][hapmap]
rs907625	0.88[LWK][hapmap];0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv892228	chr9:8482778-8703733	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv831504	chr9:8496277-8665773	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv892231	chr9:8569186-8659757	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv892232	chr9:8645448-8698875	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv892233	chr9:8645448-8702964	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv892234	chr9:8645448-8703733	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1028018	RLN1	cis	parietal	SCAN
rs1028018	PDCD1LG2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8644400-8660400	Weak transcription	Aorta	Aorta
2	chr9:8652800-8660800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:8652800-8664400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:8652800-8669000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:8653800-8660000	Weak transcription	Brain Angular Gyrus	brain
6	chr9:8653800-8660400	Weak transcription	Fetal Muscle Leg	muscle
7	chr9:8653800-8664800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:8654400-8660000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr9:8654400-8660400	Weak transcription	Ovary	ovary
10	chr9:8655600-8660000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr9:8658200-8661400	Enhancers	Brain Cingulate Gyrus	brain
12	chr9:8658800-8661000	Enhancers	Brain Substantia Nigra	brain
13	chr9:8658800-8661600	Enhancers	Brain Hippocampus Middle	brain
14	chr9:8659000-8659800	Enhancers	Fetal Brain Male	brain
15	chr9:8659000-8661000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:8659000-8661200	Enhancers	Brain Anterior Caudate	brain
17	chr9:8659600-8659800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr9:8659600-8660000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:8659600-8660200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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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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