Variant report

Variant	rs1540129
Chromosome Location	chr11:71129523-71129524
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10792680	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10898091	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1540128	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1945491	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4944043	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4944045	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4944046	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4944884	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4944890	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7105151	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7114296	0.94[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv832202	chr11:71088949-71131368	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
6	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers 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	14 gene(s)	inside rSNPs	diseases
7	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1540129	NADSYN1	cis	Nerve Tibial	GTEx
rs1540129	RP11-660L16.2	cis	Thyroid	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71123600-71139600	Weak transcription	Right Atrium	heart
2	chr11:71128600-71130800	Enhancers	Fetal Muscle Leg	muscle
3	chr11:71129000-71131800	Enhancers	Primary B cells from peripheral blood	blood
4	chr11:71129200-71129800	Enhancers	HSMMtube	muscle
5	chr11:71129200-71130600	Enhancers	Fetal Muscle Trunk	muscle
6	chr11:71129200-71131200	Enhancers	HSMM	muscle
7	chr11:71129200-71133600	Enhancers	Primary B cells from cord blood	blood
8	chr11:71129200-71134000	Enhancers	GM12878-XiMat	blood
9	chr11:71129400-71130000	Enhancers	Brain Hippocampus Middle	brain
10	chr11:71129400-71130000	Enhancers	Brain Substantia Nigra	brain
11	chr11:71129400-71130400	Enhancers	Brain Inferior Temporal Lobe	brain

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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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