Variant report

Variant	rs2886826
Chromosome Location	chr12:75920408-75920409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75919171..75922679-chr12:76098756..76100488,3	MCF-7	breast:
2	chr12:75918349..75922851-chr12:76423877..76426904,6	MCF-7	breast:
3	chr12:75920125..75921420-chr12:76430608..76431472,4	MCF-7	breast:
4	chr12:75918799..75923199-chr12:76423182..76427634,7	MCF-7	breast:
5	chr12:75919717..75922207-chr12:76426912..76429437,2	K562	blood:

Variant related genes	Relation type
ENSG00000257839	Chromatin interaction
ENSG00000139289	Chromatin interaction
ENSG00000257453	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10748282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785198	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10879929	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10879932	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10879933	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10879934	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10879935	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10879936	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11180562	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11180575	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11180584	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11180598	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11180603	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11514051	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11519910	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11520226	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12811250	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1697759	0.80[EUR][1000 genomes]
rs17115238	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054518	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2366988	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2366989	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34406885	0.86[EUR][1000 genomes]
rs3847671	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3898937	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4323912	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4882631	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58886425	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60465677	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6582293	0.85[EUR][1000 genomes]
rs7137610	0.84[EUR][1000 genomes]
rs7300994	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7305673	0.84[EUR][1000 genomes]
rs7314220	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7955264	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7956673	0.85[EUR][1000 genomes]
rs7956953	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7958508	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7962144	0.83[EUR][1000 genomes]
rs7962276	0.85[EUR][1000 genomes]
rs7979460	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7979600	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7980713	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9634253	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv428592	chr12:75766619-75936721	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2886826	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs2886826	GLIPR1L2	cis	lung	GTEx
rs2886826	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs2886826	GLIPR1L2	cis	Artery Tibial	GTEx
rs2886826	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs2886826	GLIPR1L2	cis	Thyroid	GTEx
rs2886826	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs2886826	RP11-585P4.5	cis	Artery Tibial	GTEx
rs2886826	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs2886826	GLIPR1L2	cis	Nerve Tibial	GTEx
rs2886826	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs2886826	GLIPR1L2	cis	Muscle Skeletal	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75919400-75920800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:75919400-75921000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:75919400-75922800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:75919800-75920800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:75920000-75920800	Enhancers	Fetal Heart	heart
6	chr12:75920200-75921200	Enhancers	NHDF-Ad	bronchial
7	chr12:75920400-75920600	Enhancers	Fetal Brain Male	brain
8	chr12:75920400-75920800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr12:75920400-75920800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:75920400-75920800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:75920400-75920800	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr12:75920400-75920800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:75920400-75920800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:75920400-75920800	Enhancers	Primary B cells from peripheral blood	blood
15	chr12:75920400-75920800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr12:75920400-75920800	Enhancers	Fetal Muscle Trunk	muscle
17	chr12:75920400-75920800	Enhancers	Fetal Muscle Leg	muscle
18	chr12:75920400-75920800	Enhancers	GM12878-XiMat	blood
19	chr12:75920400-75920800	Enhancers	HepG2	liver
20	chr12:75920400-75921000	Enhancers	Dnd41	blood
21	chr12:75920400-75921000	Enhancers	HSMM	muscle
22	chr12:75920400-75921000	Enhancers	NHLF	lung
23	chr12:75920400-75921200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:75920400-75921200	Enhancers	NH-A	brain
25	chr12:75920400-75921800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr12:75920400-75922800	Enhancers	A549	lung

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