Variant report

Variant	rs41530345
Chromosome Location	chr9:73071709-73071710
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10780934	0.83[EUR][1000 genomes]
rs11142419	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11142421	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13302860	0.82[MEX][hapmap]
rs1475820	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17455513	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17455773	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17534370	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60480667	0.87[ASN][1000 genomes]
rs73462451	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73462466	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73462472	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73462475	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73462480	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73462482	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7853214	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs915489	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs915490	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv428219	chr9:73006269-73192535	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41530345	MAMDC2	cis	cerebellum	SCAN
rs41530345	MAMDC2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73067600-73080400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr9:73070600-73071800	Enhancers	Fetal Stomach	stomach
3	chr9:73070600-73072800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr9:73070800-73071800	Enhancers	Duodenum Smooth Muscle	Duodenum
5	chr9:73070800-73071800	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr9:73070800-73071800	Enhancers	Stomach Mucosa	stomach
7	chr9:73070800-73072000	Enhancers	HepG2	liver
8	chr9:73071000-73071800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:73071200-73071800	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr9:73071200-73072200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:73071400-73078600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:73071400-73081800	Weak transcription	Lung	lung
13	chr9:73071600-73072400	Weak transcription	Esophagus	oesophagus
14	chr9:73071600-73073200	Weak transcription	Right Atrium	heart
15	chr9:73071600-73076800	Weak transcription	Psoas Muscle	Psoas
16	chr9:73071600-73077000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr9:73071600-73082200	Weak transcription	Pancreas	Pancrea

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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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