Variant report

Variant	rs541169
Chromosome Location	chr19:35719020-35719021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12972214	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs16970163	1.00[JPT][hapmap]
rs482324	0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs504389	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs507251	0.83[ASN][1000 genomes]
rs542977	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs564117	0.81[YRI][hapmap]
rs565704	0.81[YRI][hapmap]
rs565791	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs569596	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs8100411	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv1066553	chr19:35698638-35749563	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	esv2763203	chr19:35700047-35738400	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs541169	LSR	cis	Artery Aorta	GTEx
rs541169	IRGC	cis	cerebellum	SCAN
rs541169	AD000684.2	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35716400-35724400	Weak transcription	Lung	lung
2	chr19:35717000-35722800	Weak transcription	Spleen	Spleen
3	chr19:35717600-35720200	Enhancers	Brain Hippocampus Middle	brain
4	chr19:35717800-35720000	Enhancers	Brain Substantia Nigra	brain
5	chr19:35718200-35719200	Weak transcription	Brain Angular Gyrus	brain
6	chr19:35718600-35720000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr19:35718800-35719200	Enhancers	K562	blood
8	chr19:35718800-35719600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:35718800-35719600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:35718800-35720200	Enhancers	Brain Cingulate Gyrus	brain
11	chr19:35719000-35719800	Enhancers	HUES6 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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