Variant report

Variant	rs11238994
Chromosome Location	chr10:44829205-44829206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10900021	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10900023	0.92[EUR][1000 genomes]
rs10900024	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11238988	0.91[AFR][1000 genomes]
rs11599561	0.87[CEU][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11599730	0.88[CEU][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12355549	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12358646	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12360225	0.87[CEU][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7069891	0.87[CEU][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][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	nsv1038511	chr10:44596885-44870030	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1052337	chr10:44821390-44865015	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11238994	PNPLA6	trans	brain	seeQTL
rs11238994	PPCS	trans	brain	seeQTL
rs11238994	ZNF574	trans	brain	seeQTL
rs11238994	TMEM184C	trans	brain	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44823200-44830200	Weak transcription	Pancreas	Pancrea
2	chr10:44827800-44829800	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr10:44828200-44829600	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr10:44829000-44830200	Enhancers	Psoas Muscle	Psoas
5	chr10:44829000-44830400	Enhancers	Fetal Thymus	thymus
6	chr10:44829000-44831200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr10:44829000-44831400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:44829000-44832200	Enhancers	Fetal Muscle Trunk	muscle
9	chr10:44829000-44833600	Enhancers	Fetal Muscle Leg	muscle
10	chr10:44829200-44830000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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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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