Variant report

Variant	rs12129517
Chromosome Location	chr1:222158301-222158302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MIA3-3	chr1:222157396-222158306	XLOC_000575

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12117316	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12120736	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12122410	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12126368	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12136244	0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12137305	0.87[EUR][1000 genomes]
rs12137800	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140406	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339869	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17011253	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2153352	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185327	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2378497	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2378498	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2790762	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2800859	0.88[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2800860	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2970199	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3121626	0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5013041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55756813	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56054113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56236427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823896	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61823902	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823903	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823905	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs996854	0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014333	chr1:222131785-222245578	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222146200-222163800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:222153200-222161400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:222153200-222163800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:222154200-222160800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:222156000-222158800	Enhancers	HMEC	breast
6	chr1:222156600-222166000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:222157400-222159600	Weak transcription	NHDF-Ad	bronchial
8	chr1:222157400-222160400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:222157400-222160400	Weak transcription	HSMM	muscle
10	chr1:222157400-222160600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:222157400-222160600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:222157400-222160800	Weak transcription	Osteobl	bone
13	chr1:222157400-222161200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:222157600-222160400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:222157600-222160400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:222157600-222160600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:222157800-222160600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:222158000-222158400	Weak transcription	NHEK	skin

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