Variant report

Variant	rs12567556
Chromosome Location	chr1:67044440-67044441
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10493411	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10789211	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10889629	0.98[ASN][1000 genomes]
rs10889638	0.83[EUR][1000 genomes]
rs11208907	0.91[ASN][1000 genomes]
rs11208908	1.00[ASN][1000 genomes]
rs11208910	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208916	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11208924	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11208929	0.93[EUR][1000 genomes]
rs11208930	0.92[EUR][1000 genomes]
rs1156618	0.98[ASN][1000 genomes]
rs12023176	0.90[ASN][1000 genomes]
rs12025668	0.84[EUR][1000 genomes]
rs12034344	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039282	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12041930	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12046520	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12046904	0.84[EUR][1000 genomes]
rs12048885	0.84[EUR][1000 genomes]
rs12402181	0.93[EUR][1000 genomes]
rs12565798	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1373909	1.00[ASN][1000 genomes]
rs17129065	0.84[EUR][1000 genomes]
rs2312153	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795531	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4655498	1.00[ASN][1000 genomes]
rs4655620	1.00[ASN][1000 genomes]
rs6588209	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6680968	1.00[ASN][1000 genomes]
rs6687137	1.00[ASN][1000 genomes]
rs6697068	0.84[EUR][1000 genomes]
rs6701907	0.83[EUR][1000 genomes]
rs6701988	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72916320	0.84[EUR][1000 genomes]
rs72918447	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7512692	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7519639	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7525509	0.97[ASN][1000 genomes]
rs7535076	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7537440	0.98[ASN][1000 genomes]
rs7547794	0.98[ASN][1000 genomes]
rs7547857	0.98[ASN][1000 genomes]
rs7547866	0.98[ASN][1000 genomes]
rs7551301	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs963140	1.00[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	nsv1013351	chr1:67039730-67055937	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1003016	chr1:67043120-67067119	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12567556	SGIP1	cis	Whole Blood	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67040800-67044800	Enhancers	NHDF-Ad	bronchial
2	chr1:67041400-67045600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:67041600-67062400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:67042000-67045800	Enhancers	Primary hematopoietic stem cells	blood
5	chr1:67042000-67046200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:67042000-67046400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:67042200-67045000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:67042600-67044800	Enhancers	Osteobl	bone
9	chr1:67043000-67046600	Weak transcription	Small Intestine	intestine
10	chr1:67043200-67047600	Weak transcription	Fetal Lung	lung
11	chr1:67043200-67052000	Weak transcription	Brain Angular Gyrus	brain
12	chr1:67043200-67056800	Weak transcription	Brain Anterior Caudate	brain
13	chr1:67043200-67064400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:67043400-67045000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:67043400-67045000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:67043400-67056200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:67043600-67050600	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:67043600-67066600	Weak transcription	Fetal Brain Male	brain
19	chr1:67044000-67057200	Weak transcription	Aorta	Aorta
20	chr1:67044200-67064000	Weak transcription	NH-A	brain
21	chr1:67044400-67044600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:67044400-67045000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:67044400-67045000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:67044400-67045800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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