Variant report

Variant	rs10899040
Chromosome Location	chr11:74425096-74425097
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1433770	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1944936	0.91[CEU][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs1944937	0.91[CEU][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4944945	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7935154	0.91[CEU][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7941425	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948517	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer 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	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10899040	XRRA1	cis	parietal	SCAN
rs10899040	PLEKHB1	cis	cerebellum	SCAN
rs10899040	XRRA1	cis	lymphoblastoid	seeQTL
rs10899040	XRRA1	cis	cerebellum	SCAN
rs10899040	RAB6A	cis	parietal	SCAN
rs10899040	P2RY2	cis	parietal	SCAN
rs10899040	PAAF1	cis	cerebellum	SCAN
rs10899040	MYSM1	trans	cerebellum	SCAN
rs10899040	RNF169	cis	cerebellum	SCAN
rs10899040	FCHSD2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74422000-74427800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr11:74422000-74429000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:74422000-74430800	Weak transcription	Right Atrium	heart
4	chr11:74422400-74427800	Weak transcription	Ovary	ovary
5	chr11:74422400-74427800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr11:74422400-74427800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:74422400-74428400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:74422400-74428600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:74422400-74430800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:74422600-74427800	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:74422600-74427800	Weak transcription	Fetal Intestine Small	intestine
12	chr11:74423400-74427200	Weak transcription	Fetal Stomach	stomach
13	chr11:74424400-74425200	Enhancers	HSMMtube	muscle

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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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