Variant report

Variant	rs4643650
Chromosome Location	chr3:34850303-34850304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10510661	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12495914	0.90[ASN][1000 genomes]
rs2035646	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6550303	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6774675	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6774848	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6784786	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6789009	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6801611	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6805290	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6810327	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs73061031	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834654	chr3:34747802-34916657	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv834655	chr3:34752929-34898824	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv3415700	chr3:34806371-34914306	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1010956	chr3:34833573-34878681	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
5	esv3408584	chr3:34838963-34881489	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4643650	SCN10A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:34848800-34850400	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr3:34848800-34850400	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr3:34849000-34850600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:34849000-34850600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:34849200-34850400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:34849200-34850600	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:34849400-34852600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:34849400-34855200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:34849600-34850400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr3:34849800-34850400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr3:34850200-34850400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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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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