Variant report

Variant	rs9811344
Chromosome Location	chr3:112845175-112845176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12486277	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs13071497	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17316696	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795161	0.80[ASN][1000 genomes]
rs1797620	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1881943	0.90[JPT][hapmap]
rs2700208	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28645753	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35097436	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6783663	0.91[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9810734	0.87[CEU][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9829983	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs9834189	0.91[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[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	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	nsv877344	chr3:112789865-112854339	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv877345	chr3:112826253-112848851	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv518148	chr3:112845175-112846786	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9811344	ATP6V1A	cis	cerebellum	SCAN
rs9811344	RP11-572M11.3	cis	Esophagus Muscularis	GTEx
rs9811344	KIAA1407	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112840600-112846800	Weak transcription	Fetal Stomach	stomach
2	chr3:112842800-112845600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:112843200-112847200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:112843400-112847000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:112843400-112851200	Weak transcription	NHEK	skin
6	chr3:112843600-112847000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:112843800-112846800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:112843800-112847000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:112843800-112847000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:112843800-112847000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:112844200-112847000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:112844800-112845600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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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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