Variant report

Variant	rs2123534
Chromosome Location	chr15:40814324-40814325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1051482	0.90[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs10851396	0.85[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11070279	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11070280	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11852527	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11857247	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12148185	0.86[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs12899408	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12907448	0.83[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs12907984	0.81[AMR][1000 genomes]
rs12908114	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12908867	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12914501	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12915563	0.88[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12916323	0.91[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1453183	0.90[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17746659	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17747399	0.81[AMR][1000 genomes]
rs1901774	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2412524	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3213999	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34303240	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34750756	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35030447	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35884042	0.81[AMR][1000 genomes]
rs36122190	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3743146	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3803353	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4457966	0.86[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs55954396	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56384845	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61048252	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62018030	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62018046	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62018048	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018051	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62019866	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62019883	0.85[AMR][1000 genomes]
rs7162749	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7164385	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7165054	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7181909	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72733469	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs731640	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs733299	0.90[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8025458	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs8028910	0.91[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8036938	0.85[EUR][1000 genomes]
rs8042733	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9672313	0.80[CEU][hapmap]
rs9806410	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs999197	0.91[CEU][hapmap];0.86[EUR][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	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs2123534	CCDC32	cis	multi-tissue	Pritchard
rs2123534	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs2123534	CCDC32	cis	normal skin	skin_eQTL
rs2123534	CCDC32	cis	lesional skin	skin_eQTL
rs2123534	C15orf57	cis	Cerebellum	GTEx
rs2123534	C15orf57	cis	Nerve Tibial	GTEx
rs2123534	RP11-111A22.1	cis	Artery Tibial	GTEx
rs2123534	C15orf57	cis	lung	GTEx
rs2123534	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs2123534	C15orf57	cis	Artery Tibial	GTEx
rs2123534	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs2123534	C15orf57	cis	Esophagus Muscularis	GTEx
rs2123534	ZFYVE19	cis	multi-tissue	Pritchard
rs2123534	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs2123534	RP11-111A22.1	cis	lung	GTEx
rs2123534	MGC20481	cis	multi-tissue	Pritchard
rs2123534	KNSTRN	cis	Heart Left Ventricle	GTEx
rs2123534	C15orf57	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40804400-40821000	Weak transcription	Right Atrium	heart
2	chr15:40805200-40828200	Weak transcription	Placenta	Placenta
3	chr15:40805200-40833000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:40812400-40814400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr15:40812400-40817800	Weak transcription	Esophagus	oesophagus
6	chr15:40812400-40817800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr15:40812400-40817800	Weak transcription	Pancreas	Pancrea
8	chr15:40812400-40818800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:40812400-40820200	Weak transcription	Fetal Stomach	stomach
10	chr15:40812400-40828600	Weak transcription	Primary T cells from cord blood	blood
11	chr15:40812400-40828600	Weak transcription	Right Ventricle	heart
12	chr15:40812400-40828800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:40812400-40828800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr15:40812400-40829000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:40812400-40829000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:40812400-40831000	Weak transcription	Thymus	Thymus
17	chr15:40812400-40837800	Weak transcription	Lung	lung
18	chr15:40812600-40814400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr15:40812600-40818200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:40812600-40826000	Weak transcription	Adipose Nuclei	Adipose
21	chr15:40812600-40826400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr15:40812600-40827000	Weak transcription	Spleen	Spleen
23	chr15:40812600-40831400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:40812600-40840600	Weak transcription	Hela-S3	cervix
25	chr15:40813400-40815000	Weak transcription	GM12878-XiMat	blood

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