Variant report

Variant	rs12153000
Chromosome Location	chr5:80815467-80815468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACOT12-9	chr5:80813191-80815724	NONHSAT102466

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10036712	0.93[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10041030	0.93[JPT][hapmap]
rs10042303	1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10075648	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs10454898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474031	0.93[JPT][hapmap]
rs11739075	0.92[JPT][hapmap]
rs12188888	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12697705	0.86[JPT][hapmap]
rs1541830	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs2162973	0.93[JPT][hapmap]
rs2972228	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972230	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972232	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2972244	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2972245	0.84[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2973341	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2973343	0.88[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2973347	0.85[TSI][hapmap]
rs2973350	0.84[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34414290	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4529168	0.80[CHD][hapmap]
rs6452411	0.93[JPT][hapmap]
rs6452412	0.93[JPT][hapmap]
rs6452414	0.87[CHD][hapmap];0.93[JPT][hapmap]
rs6452415	0.93[JPT][hapmap]
rs6452416	0.80[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6868422	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs6868748	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs6872775	0.83[JPT][hapmap]
rs6877102	0.93[JPT][hapmap]
rs6878037	0.80[CEU][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6880200	0.92[JPT][hapmap]
rs6883488	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs6887937	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs6897189	0.93[JPT][hapmap]
rs7711020	0.80[JPT][hapmap]
rs7719373	0.81[CHD][hapmap];0.92[JPT][hapmap]
rs7733938	1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9293275	0.87[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs9596	0.93[JPT][hapmap]
rs964102	0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1028498	chr5:80712364-80860430	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12153000	C19orf24	trans	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80779000-80830200	Weak transcription	Primary B cells from cord blood	blood
2	chr5:80779000-80834400	Weak transcription	Fetal Muscle Leg	muscle
3	chr5:80797000-80834000	Weak transcription	Primary B cells from peripheral blood	blood
4	chr5:80798200-80818000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:80798400-80820000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr5:80798400-80821400	Weak transcription	Thymus	Thymus
7	chr5:80798600-80826600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:80802000-80819600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:80802600-80819800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:80803200-80834400	Weak transcription	Fetal Kidney	kidney
11	chr5:80803200-80835200	Weak transcription	GM12878-XiMat	blood
12	chr5:80803600-80875200	Weak transcription	Fetal Brain Female	brain
13	chr5:80808600-80818600	Weak transcription	Fetal Thymus	thymus
14	chr5:80809600-80820200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:80809800-80820000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:80811000-80816600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:80812400-80826600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:80812400-80829200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:80812600-80821400	Weak transcription	HSMM	muscle
20	chr5:80813600-80818400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:80815200-80815600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:80815200-80815600	Enhancers	HSMMtube	muscle
23	chr5:80815200-80817000	Enhancers	Dnd41	blood

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