Variant report

Variant	rs12141009
Chromosome Location	chr1:47495822-47495823
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47481637..47484566-chr1:47494285..47496054,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1021827	0.89[GIH][hapmap]
rs1039468	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1039469	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10890445	0.89[GIH][hapmap]
rs11211420	0.82[JPT][hapmap]
rs11211422	0.84[GIH][hapmap];0.89[TSI][hapmap]
rs11211424	0.82[JPT][hapmap]
rs11211436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs11211441	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11211445	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11582907	0.82[JPT][hapmap]
rs12026359	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[LWK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap]
rs12030385	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041262	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12041324	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12045381	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12140891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12406683	0.82[JPT][hapmap]
rs1502909	0.90[CHB][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes]
rs1553390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17102972	0.82[JPT][hapmap]
rs17102977	0.82[JPT][hapmap]
rs17102978	0.82[JPT][hapmap]
rs1827473	0.86[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1847225	0.95[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs1963620	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1986925	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2036462	1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2292059	0.88[JPT][hapmap]
rs2292060	0.82[JPT][hapmap]
rs2897114	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4926728	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4926776	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55909645	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66753730	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6682257	0.81[EUR][1000 genomes]
rs72637973	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9326151	0.89[GIH][hapmap]
rs9326152	0.89[GIH][hapmap]
rs9699826	0.82[JPT][hapmap]
rs9699991	0.82[JPT][hapmap]
rs9701888	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9793989	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871958	chr1:47350374-47517123	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1009338	chr1:47358532-47555253	Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2763300	chr1:47358532-47628774	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv870695	chr1:47363893-47502714	Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv871288	chr1:47363893-47507808	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv871377	chr1:47363893-47517123	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv870674	chr1:47416441-47517123	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv871717	chr1:47449486-47524264	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv461428	chr1:47487585-47524264	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv546167	chr1:47487585-47524264	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv871080	chr1:47489786-47517123	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12141009	SPATA6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47490000-47496600	Weak transcription	Esophagus	oesophagus
2	chr1:47490000-47496600	Weak transcription	Right Atrium	heart
3	chr1:47490400-47500400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:47490600-47498600	Weak transcription	Brain Anterior Caudate	brain
5	chr1:47491000-47496000	Weak transcription	Psoas Muscle	Psoas
6	chr1:47491000-47501600	Weak transcription	Gastric	stomach
7	chr1:47491600-47517200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:47494600-47496400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:47494800-47497000	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr1:47494800-47497600	Enhancers	HUVEC	blood vessel
11	chr1:47495000-47496600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:47495200-47497600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr1:47495200-47498600	Enhancers	HMEC	breast
14	chr1:47495200-47499000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:47495600-47496400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:47495600-47496600	Enhancers	Hela-S3	cervix
17	chr1:47495600-47496600	Enhancers	NHEK	skin
18	chr1:47495600-47497800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:47495800-47496000	Enhancers	Brain Angular Gyrus	brain
20	chr1:47495800-47497400	Enhancers	Adipose Nuclei	Adipose
21	chr1:47495800-47497600	Enhancers	Aorta	Aorta
22	chr1:47495800-47497600	Enhancers	Stomach Mucosa	stomach
23	chr1:47495800-47497800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:47495800-47498400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:47495800-47498600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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