Variant report

Variant	rs12431821
Chromosome Location	chr14:81272588-81272589
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10136404	0.82[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs1016507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1025253	0.82[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap]
rs1035144	0.81[JPT][hapmap]
rs11623023	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11623416	0.80[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs12432357	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12434564	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12878945	0.83[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap]
rs12880014	1.00[CHB][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes]
rs12880075	0.80[ASN][1000 genomes]
rs12886388	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12888082	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12891585	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12892825	0.80[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap]
rs12895801	0.80[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs12896065	0.85[AMR][1000 genomes]
rs1458993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1597320	0.87[CHB][hapmap];0.87[YRI][hapmap]
rs17111270	0.80[CEU][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap]
rs172920	0.88[EUR][1000 genomes]
rs17542615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17542712	0.83[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap]
rs17613911	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs17614081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1797670	0.85[CHB][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1992973	0.83[AMR][1000 genomes]
rs2044737	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2044738	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2114703	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs2215981	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs2217174	0.83[EUR][1000 genomes]
rs2217176	0.96[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2246617	0.86[CHB][hapmap];0.85[YRI][hapmap]
rs228110	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs228111	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs228118	0.88[EUR][1000 genomes]
rs228120	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[EUR][1000 genomes]
rs228121	0.88[EUR][1000 genomes]
rs228125	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.88[EUR][1000 genomes]
rs2371413	0.86[CHB][hapmap];0.87[YRI][hapmap]
rs2371416	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2371457	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[EUR][1000 genomes]
rs2371462	0.80[CEU][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs2556601	0.88[EUR][1000 genomes]
rs2556605	0.85[EUR][1000 genomes]
rs2590480	0.91[ASW][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap]
rs2596118	0.83[AMR][1000 genomes]
rs2888046	0.90[JPT][hapmap]
rs35540104	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3742721	0.80[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap]
rs3742722	0.80[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap]
rs4411444	0.81[JPT][hapmap]
rs4523859	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4899782	0.80[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4903948	0.96[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap]
rs4903954	0.88[JPT][hapmap]
rs61979448	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61979449	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61979451	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61979452	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6574605	0.91[ASW][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap]
rs6574613	0.88[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs66492142	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7141130	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7141434	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs71416852	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7143407	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7148368	0.96[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7148618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7150858	0.88[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.87[ASN][1000 genomes]
rs7153979	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs7154132	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs7154373	0.82[EUR][1000 genomes]
rs728444	0.82[EUR][1000 genomes]
rs759916	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs759917	0.83[EUR][1000 genomes]
rs8003784	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8005809	0.87[CHB][hapmap];0.85[YRI][hapmap]
rs8005883	0.80[EUR][1000 genomes]
rs8006507	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8006864	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8009120	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs8016601	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs8021137	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs8022411	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[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	nsv869348	chr14:80921098-81535754	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv832840	chr14:81270033-81423583	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12431821	C14orf179	cis	cerebellum	SCAN
rs12431821	VIPAR	cis	parietal	SCAN
rs12431821	C14orf145	cis	cerebellum	SCAN
rs12431821	C14orf145	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:81192800-81305400	Weak transcription	Primary B cells from cord blood	blood
2	chr14:81251800-81282600	Weak transcription	A549	lung
3	chr14:81259400-81274000	Weak transcription	Aorta	Aorta
4	chr14:81259400-81274000	Weak transcription	Pancreas	Pancrea
5	chr14:81259400-81274200	Weak transcription	Thymus	Thymus
6	chr14:81259400-81278400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr14:81265600-81277200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr14:81265600-81284400	Weak transcription	Fetal Thymus	thymus
9	chr14:81265800-81274600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr14:81267400-81273800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr14:81267400-81284200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:81267400-81284800	Weak transcription	HSMM	muscle
13	chr14:81269600-81273000	Weak transcription	Fetal Lung	lung
14	chr14:81269600-81284400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr14:81270200-81273600	Weak transcription	Dnd41	blood
16	chr14:81272200-81274200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr14:81272200-81284600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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