Variant report

Variant	rs1843399
Chromosome Location	chr3:59777008-59777009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2629878	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2629879	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2629881	0.94[EUR][1000 genomes]
rs4455289	0.83[EUR][1000 genomes]
rs562516	1.00[CEU][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs606415	0.90[EUR][1000 genomes]
rs6781354	0.86[CEU][hapmap]
rs683809	0.91[EUR][1000 genomes]
rs9311726	0.95[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][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	nsv1014601	chr3:59666609-59888166	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv1003387	chr3:59756364-59831340	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv460562	chr3:59760118-59826778	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv590381	chr3:59760118-59826778	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv590382	chr3:59763809-59793062	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
6	nsv460563	chr3:59772342-59827390	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv590383	chr3:59772342-59827390	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1843399	ID2B	cis	cerebellum	SCAN
rs1843399	PTPRG	cis	parietal	SCAN
rs1843399	IL17RD	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59769800-59791400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr3:59770000-59779000	Weak transcription	Thymus	Thymus
3	chr3:59770400-59825200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:59775400-59777200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr3:59775600-59777400	Enhancers	Fetal Thymus	thymus
6	chr3:59775600-59777400	Enhancers	Dnd41	blood
7	chr3:59776600-59778200	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr3:59776800-59777200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:59776800-59787000	Weak transcription	Primary T cells from cord blood	blood
10	chr3:59777000-59781800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:59777000-59786800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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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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