Variant report

Variant	rs6425276
Chromosome Location	chr1:171447265-171447266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10913129	0.81[CEU][hapmap];0.90[AMR][1000 genomes]
rs12124034	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12126218	0.81[AMR][1000 genomes]
rs12126599	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12128241	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12134052	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12136219	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12145006	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12145591	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12146098	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12403390	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1387832	0.81[CEU][hapmap]
rs17586576	0.81[CEU][hapmap]
rs17646340	0.92[CEU][hapmap];0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6425276	HMGB1P11	cis	Nerve Tibial	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171445600-171447400	Enhancers	HSMMtube	muscle
2	chr1:171446200-171447400	Enhancers	K562	blood
3	chr1:171446400-171449000	Weak transcription	Fetal Kidney	kidney
4	chr1:171446600-171449200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:171447000-171447600	Enhancers	HepG2	liver

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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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