Variant report

Variant	rs9810734
Chromosome Location	chr3:112874860-112874861
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12486277	0.92[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs17316696	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1797620	0.82[EUR][1000 genomes]
rs1881943	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs1920080	0.89[ASN][1000 genomes]
rs2613963	0.89[ASN][1000 genomes]
rs2700208	0.81[EUR][1000 genomes]
rs28645753	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35097436	0.83[EUR][1000 genomes]
rs6783663	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9811344	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9829983	0.92[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs9834189	0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9810734	KIAA1407	cis	parietal	SCAN
rs9810734	RP11-572M11.3	cis	Esophagus Muscularis	GTEx
rs9810734	ATP6V1A	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112871000-112876600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:112871000-112881400	Weak transcription	Fetal Lung	lung
3	chr3:112871400-112875800	Weak transcription	Fetal Stomach	stomach
4	chr3:112871400-112876000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:112871400-112876000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:112871600-112875200	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:112872400-112876000	Weak transcription	Adipose Nuclei	Adipose
8	chr3:112873000-112875600	Weak transcription	Fetal Kidney	kidney
9	chr3:112873000-112875800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:112873000-112875800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:112873000-112876000	Weak transcription	HSMMtube	muscle
12	chr3:112873000-112876200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:112873200-112875800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:112873400-112876000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:112874800-112875000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:112874800-112876600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:112874800-112877600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:112874800-112878000	Enhancers	Colon Smooth Muscle	Colon

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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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