Variant report

Variant	rs12302010
Chromosome Location	chr12:29193136-29193137
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10734770	0.89[EUR][1000 genomes]
rs10743643	0.87[EUR][1000 genomes]
rs11049980	0.84[ASN][1000 genomes]
rs11049992	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050084	1.00[JPT][hapmap]
rs11502454	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12298186	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12298377	0.84[ASN][1000 genomes]
rs12302231	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305429	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12309591	0.86[EUR][1000 genomes]
rs12311115	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320204	0.82[EUR][1000 genomes]
rs1353460	0.87[EUR][1000 genomes]
rs1390542	0.87[EUR][1000 genomes]
rs1496221	0.87[EUR][1000 genomes]
rs1561131	1.00[JPT][hapmap]
rs1561132	1.00[JPT][hapmap]
rs17449204	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17449238	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1865763	0.87[EUR][1000 genomes]
rs1865764	0.89[EUR][1000 genomes]
rs2164493	0.89[EUR][1000 genomes]
rs2196479	0.89[EUR][1000 genomes]
rs2349971	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs28544897	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3940535	0.87[EUR][1000 genomes]
rs4930849	0.89[EUR][1000 genomes]
rs4930856	1.00[JPT][hapmap]
rs4931154	0.87[EUR][1000 genomes]
rs59113616	0.81[EUR][1000 genomes]
rs60329521	0.87[EUR][1000 genomes]
rs6487757	0.89[EUR][1000 genomes]
rs6487764	0.81[EUR][1000 genomes]
rs66487137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66712682	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67060812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67087836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67287552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67563394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67760969	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716704	0.89[EUR][1000 genomes]
rs7304088	0.89[EUR][1000 genomes]
rs73061737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73061745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315912	0.86[EUR][1000 genomes]
rs7316030	0.87[EUR][1000 genomes]
rs73254758	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73254786	0.87[EUR][1000 genomes]
rs73268857	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73268858	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73273123	0.82[EUR][1000 genomes]
rs7964313	0.87[EUR][1000 genomes]
rs7966290	0.89[EUR][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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers 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 target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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 target site	35 gene(s)	inside rSNPs	diseases
3	esv2758301	chr12:29110782-29289849	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2759888	chr12:29110782-29289849	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12302010	BICD1	cis	parietal	SCAN
rs12302010	IFLTD1	cis	parietal	SCAN
rs12302010	ERGIC2	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29190000-29194200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr12:29191400-29194200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:29191400-29197200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:29191600-29194400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:29191600-29196000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:29191800-29194800	Enhancers	Fetal Intestine Large	intestine
7	chr12:29191800-29194800	Enhancers	Fetal Intestine Small	intestine
8	chr12:29191800-29197000	Enhancers	NHLF	lung
9	chr12:29192400-29193200	Enhancers	Fetal Stomach	stomach
10	chr12:29192400-29194400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:29192600-29193200	Enhancers	Fetal Muscle Leg	muscle
12	chr12:29192600-29194400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:29192600-29194600	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr12:29192600-29195600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:29192800-29193800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:29192800-29193800	Weak transcription	Osteobl	bone
17	chr12:29192800-29194200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:29192800-29194400	Weak transcription	Fetal Kidney	kidney
19	chr12:29192800-29194400	Enhancers	NHDF-Ad	bronchial
20	chr12:29193000-29194400	Enhancers	Rectal Mucosa Donor 31	rectum

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