Variant report

Variant	rs6541379
Chromosome Location	chr1:93896765-93896766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11164939	0.91[CEU][hapmap];0.93[MEX][hapmap]
rs12033147	0.90[CEU][hapmap]
rs1426317	1.00[YRI][hapmap]
rs17109958	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs237437	1.00[YRI][hapmap]
rs2433279	0.82[AMR][1000 genomes]
rs2449376	1.00[YRI][hapmap]
rs2818971	1.00[YRI][hapmap]
rs3767966	1.00[CEU][hapmap];0.93[MEX][hapmap]
rs3904666	0.90[CEU][hapmap];0.81[GIH][hapmap]
rs4847425	0.80[AMR][1000 genomes]
rs61780647	0.84[AMR][1000 genomes]
rs810027	0.90[CEU][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv3375834	chr1:93872980-93904647	ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6541379	DR1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93893600-93898000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:93893600-93899200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:93893600-93899200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:93893600-93899400	Weak transcription	ES-UCSF4 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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