Variant report

Variant	rs11054901
Chromosome Location	chr12:12577950-12577951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10772567	1.00[YRI][hapmap]
rs10845544	1.00[YRI][hapmap]
rs11054979	0.82[CEU][hapmap]
rs17312055	1.00[CEU][hapmap];0.94[AMR][1000 genomes]
rs2013675	1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs4570678	1.00[CEU][hapmap]
rs55946646	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56188411	0.82[AMR][1000 genomes]
rs56325045	0.82[AMR][1000 genomes]
rs61913515	0.83[ASN][1000 genomes]

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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11054901	LOH12CR1	cis	multi-tissue	Pritchard
rs11054901	LOH12CR1	cis	Liver	GTEx
rs11054901	LOH12CR1	cis	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12558000-12586000	Weak transcription	Pancreas	Pancrea
2	chr12:12565200-12585000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:12572600-12588400	Weak transcription	Primary T cells from cord blood	blood
4	chr12:12577000-12578000	Weak transcription	Aorta	Aorta
5	chr12:12577200-12578600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:12577400-12582200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:12577400-12582600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:12577600-12580600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:12577600-12583800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:12577800-12578000	Weak transcription	Primary B cells from cord blood	blood
11	chr12:12577800-12578200	Enhancers	Left Ventricle	heart
12	chr12:12577800-12578800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:12577800-12579200	Enhancers	Brain Anterior Caudate	brain
14	chr12:12577800-12579200	Enhancers	Osteobl	bone
15	chr12:12577800-12580000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:12577800-12581800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr12:12577800-12584000	Weak transcription	Primary T helper naive 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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