Variant report

Variant	rs4968957
Chromosome Location	chr17:66799953-66799954
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11650010	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11657619	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12450787	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12452140	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35131140	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35295565	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968950	0.80[ASN][1000 genomes]
rs4968953	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968955	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968956	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55982272	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9302983	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9894084	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9894119	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9898028	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9902321	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9905519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv575927	chr17:66787428-66817866	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4968957	NOL11	cis	cerebellum	SCAN
rs4968957	ABCA8	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66788000-66805800	Weak transcription	Right Atrium	heart
2	chr17:66792600-66803200	Weak transcription	HepG2	liver
3	chr17:66797000-66803200	Weak transcription	Adipose Nuclei	Adipose
4	chr17:66797800-66800400	Enhancers	Ovary	ovary
5	chr17:66798200-66803600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr17:66799200-66800000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr17:66799200-66800000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr17:66799200-66800000	Enhancers	Fetal Heart	heart
9	chr17:66799200-66800400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:66799200-66800400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr17:66799400-66800000	Enhancers	Fetal Muscle Leg	muscle
12	chr17:66799400-66800400	Enhancers	Brain Hippocampus Middle	brain
13	chr17:66799400-66804000	Enhancers	Fetal Brain Male	brain
14	chr17:66799600-66800000	Enhancers	Brain Anterior Caudate	brain
15	chr17:66799800-66800200	Enhancers	Brain Cingulate Gyrus	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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