Variant report

Variant	rs10771431
Chromosome Location	chr12:9380859-9380860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10771415	0.89[GIH][hapmap]
rs10771418	0.81[CEU][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap]
rs10843144	0.87[GIH][hapmap]
rs10843149	0.81[EUR][1000 genomes]
rs10843175	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1117735	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11611670	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17202253	0.81[EUR][1000 genomes]
rs17794353	0.82[CEU][hapmap]
rs1988852	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3759274	0.83[YRI][hapmap]
rs7137443	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7300786	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7300939	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7301059	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7976807	0.83[GIH][hapmap]
rs7978537	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7978746	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv527404	chr12:9250601-9435244	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
7	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
8	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
10	nsv8903	chr12:9375688-9381273	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Breast size	22747683	GWAS catalog

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10771431		cis	Lymphoblastoid	GTEx
rs10771431	DDX12P	cis	Muscle Skeletal	GTEx
rs10771431	DDX12P	cis	Artery Tibial	GTEx
rs10771431	RP11-22B23.1	cis	lung	GTEx
rs10771431	RP11-22B23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10771431	RP11-22B23.1	cis	Whole Blood	GTEx
rs10771431	RP11-22B23.1	cis	Nerve Tibial	GTEx
rs10771431	CLEC4C	cis	cerebellum	SCAN
rs10771431	ETV6	cis	parietal	SCAN
rs10771431	RP11-22B23.1	cis	Artery Tibial	GTEx
rs10771431	RP11-22B23.1	cis	Muscle Skeletal	GTEx
rs10771431	RP11-22B23.1	cis	Thyroid	GTEx
rs10771431	FAM90A1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9357400-9384800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr12:9374400-9392600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:9376200-9392600	Weak transcription	Primary T cells from cord blood	blood
4	chr12:9379200-9385800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr12:9380200-9381200	Enhancers	Fetal Lung	lung
6	chr12:9380200-9386000	Weak transcription	Spleen	Spleen
7	chr12:9380400-9381400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:9380600-9381000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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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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