Variant report

Variant	rs11197612
Chromosome Location	chr10:118024319-118024320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10218849	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10787638	1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs10787639	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10885889	0.93[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs10885907	1.00[YRI][hapmap]
rs11197611	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11197620	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11599593	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12413585	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs12773105	0.81[GIH][hapmap]
rs12774375	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1419874	0.83[ASN][1000 genomes]
rs2901100	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2901101	1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs3740572	1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs4554795	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs4751959	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7078853	1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs7087136	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3449389	chr10:117806874-118102404	Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv832000	chr10:117944492-118116253	Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1043339	chr10:118010822-118025492	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv519769	chr10:118022076-118024544	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11197612	TRUB1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:118016200-118024400	Weak transcription	HSMM	muscle
2	chr10:118017600-118024800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:118017600-118025000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr10:118019200-118028800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr10:118020600-118030200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr10:118021800-118028800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:118022200-118026000	Strong transcription	Fetal Stomach	stomach
8	chr10:118022200-118027400	Strong transcription	Fetal Muscle Leg	muscle
9	chr10:118022200-118028200	Strong transcription	Liver	Liver
10	chr10:118022200-118028400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr10:118023000-118028800	Weak transcription	Fetal Kidney	kidney
12	chr10:118023400-118030400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr10:118023800-118026600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr10:118023800-118030200	Weak transcription	HSMMtube	muscle

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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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