Variant report

Variant	rs10841886
Chromosome Location	chr12:21864377-21864378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10770848	0.91[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap]
rs10770851	0.82[ASN][1000 genomes]
rs10841872	1.00[CHB][hapmap]
rs10841878	0.82[ASN][1000 genomes]
rs10841880	0.82[ASN][1000 genomes]
rs10841887	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841889	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841890	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841891	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10841893	0.85[CEU][hapmap]
rs11046157	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs11046159	0.86[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap]
rs11046160	0.94[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs11046164	0.82[ASN][1000 genomes]
rs11046166	0.86[ASN][1000 genomes]
rs11046171	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11046172	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11046173	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11046174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426310	0.81[ASN][1000 genomes]
rs12426826	0.81[ASN][1000 genomes]
rs12816929	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821277	0.84[CEU][hapmap]
rs12824788	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs1293188	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153941	0.90[CHB][hapmap]
rs1586844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1650307	0.90[CHB][hapmap]
rs1677091	0.81[CHB][hapmap]
rs2077105	0.82[ASN][1000 genomes]
rs2638441	0.81[CHD][hapmap]
rs34015001	0.81[ASN][1000 genomes]
rs34084105	0.82[ASN][1000 genomes]
rs4148679	0.81[CHD][hapmap]
rs66592830	0.81[ASN][1000 genomes]
rs7133519	0.86[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap]
rs7135965	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs7301883	0.91[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap]
rs7305475	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7309274	1.00[YRI][hapmap]
rs731304	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7316669	0.91[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap]
rs7953579	0.91[CHB][hapmap]
rs829060	0.81[CHD][hapmap]
rs852815	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852816	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv469164	chr12:21688900-21966701	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv557744	chr12:21688900-21966701	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv832349	chr12:21749093-21930695	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10841886	RP11-59N23.3	cis	lung	GTEx
rs10841886	ABCC9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21862000-21864400	Enhancers	Fetal Lung	lung
2	chr12:21862400-21864600	Enhancers	Adipose Nuclei	Adipose
3	chr12:21862800-21864800	Enhancers	Rectal Smooth Muscle	rectum
4	chr12:21862800-21871200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:21863800-21864600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:21864000-21864400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:21864000-21864400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:21864000-21864400	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr12:21864000-21864800	Enhancers	Colon Smooth Muscle	Colon
10	chr12:21864000-21864800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:21864000-21864800	Enhancers	NHDF-Ad	bronchial
12	chr12:21864200-21864400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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