Variant report

Variant	rs4075663
Chromosome Location	chr11:18793399-18793400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12792107	0.92[YRI][hapmap]
rs4073915	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs4265582	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs56295396	0.84[AMR][1000 genomes]
rs6483525	0.91[YRI][hapmap]
rs7932701	0.89[YRI][hapmap]
rs7932996	1.00[YRI][hapmap]

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	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv525452	chr11:18735947-18802503	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv525199	chr11:18793360-18793399	Weak transcription Enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4075663	CA4	trans	brain	seeQTL
rs4075663	REC8	trans	brain	seeQTL
rs4075663	MYOD1	cis	parietal	SCAN
rs4075663	SEMA3G	trans	brain	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18783000-18801800	Weak transcription	Spleen	Spleen
2	chr11:18784000-18808000	Weak transcription	Fetal Brain Female	brain
3	chr11:18785600-18793400	Weak transcription	Fetal Brain Male	brain
4	chr11:18790800-18794000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr11:18790800-18795000	Weak transcription	Brain Anterior Caudate	brain
6	chr11:18790800-18811400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:18791800-18793400	Strong transcription	Brain Germinal Matrix	brain
8	chr11:18792000-18794000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:18792400-18794000	Enhancers	GM12878-XiMat	blood
10	chr11:18792400-18794200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr11:18792800-18793600	Enhancers	Brain Angular Gyrus	brain
12	chr11:18793000-18794600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr11:18793200-18793800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

Quick Search:

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

what's new

Quick links