Variant report

Variant	rs6424930
Chromosome Location	chr1:184158796-184158797
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1078925	0.92[ASN][1000 genomes]
rs11576332	0.82[JPT][hapmap]
rs11582961	0.82[JPT][hapmap]
rs12402790	0.82[JPT][hapmap]
rs12729638	0.82[JPT][hapmap]
rs12751711	0.82[JPT][hapmap]
rs1409812	0.82[JPT][hapmap]
rs16822379	0.82[JPT][hapmap]
rs2019378	0.92[ASN][1000 genomes]
rs34584127	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35999930	0.86[EUR][1000 genomes]
rs73055581	0.92[ASN][1000 genomes]
rs765224	0.82[JPT][hapmap]
rs765225	0.82[JPT][hapmap]

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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1006655	chr1:183922288-184186677	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv818622	chr1:184144995-184158796	Weak transcription Bivalent Enhancer Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6424930	GJA4	trans	brain	seeQTL
rs6424930	GPR146	trans	brain	seeQTL
rs6424930	FAM89A	trans	cerebellum	SCAN
rs6424930	C1orf125	cis	parietal	SCAN
rs6424930	ATP7B	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184157000-184162000	Weak transcription	Right Ventricle	heart
2	chr1:184157000-184162200	Weak transcription	Left Ventricle	heart
3	chr1:184157800-184160000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:184157800-184160000	Weak transcription	NHLF	lung
5	chr1:184157800-184162400	Enhancers	Fetal Heart	heart
6	chr1:184158200-184159400	Enhancers	Fetal Brain Male	brain
7	chr1:184158600-184159000	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr1:184158600-184159000	Enhancers	Fetal Lung	lung
9	chr1:184158600-184159600	Weak transcription	Brain Germinal Matrix	brain
10	chr1:184158600-184160800	Enhancers	Fetal Brain Female	brain
11	chr1:184158600-184163200	Enhancers	Fetal Stomach	stomach

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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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