Variant report

Variant	rs1474356
Chromosome Location	chr7:109218682-109218683
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1404133	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1524270	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1524272	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1721897	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1721902	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1721977	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1815091	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2091134	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3938257	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6466288	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7779039	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs940363	0.87[EUR][1000 genomes]
rs940364	0.82[AMR][1000 genomes];0.85[EUR][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	nsv1023379	chr7:109003574-109355234	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv608079	chr7:109098364-109862289	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1020761	chr7:109208187-109275700	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1474356	SLC26A3	cis	cerebellum	SCAN
rs1474356	RINT1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:109211800-109234000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:109212000-109219800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr7:109212400-109219000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:109215200-109219400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:109217400-109220400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr7:109217800-109218800	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr7:109218000-109223800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr7:109218200-109225000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr7:109218200-109226400	Weak transcription	HUES48 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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