Variant report

Variant	rs12054001
Chromosome Location	chr3:112389564-112389565
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112385289..112387642-chr3:112388992..112390614,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11927615	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054416	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1249910	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249929	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13068244	0.82[EUR][1000 genomes]
rs13077054	0.93[EUR][1000 genomes]
rs13088866	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092258	0.83[EUR][1000 genomes]
rs17457593	0.90[ASN][1000 genomes]
rs2399449	0.84[ASN][1000 genomes]
rs28374264	0.90[ASN][1000 genomes]
rs3843366	0.88[ASN][1000 genomes]
rs4145150	0.84[ASN][1000 genomes]
rs4145151	0.84[ASN][1000 genomes]
rs55894063	0.84[ASN][1000 genomes]
rs56302621	0.89[ASN][1000 genomes]
rs60397548	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768072	0.80[CEU][hapmap]
rs6772102	0.82[ASN][1000 genomes]
rs72943992	0.88[ASN][1000 genomes]
rs9818848	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs9821161	0.91[EUR][1000 genomes]
rs9821338	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs9833456	0.84[EUR][1000 genomes]
rs9842816	0.90[ASN][1000 genomes]
rs9845240	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9859566	0.91[EUR][1000 genomes]
rs9864580	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9864774	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9864845	0.83[ASN][1000 genomes]
rs9876497	0.90[CEU][hapmap];0.85[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	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112385800-112389800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:112387000-112391200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:112387600-112390400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:112388000-112395800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:112388600-112389800	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr3:112388600-112392200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr3:112388600-112393200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr3:112388800-112391400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:112388800-112392000	Enhancers	K562	blood
10	chr3:112389000-112391400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:112389000-112391600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:112389000-112392800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:112389000-112393400	Enhancers	Primary T cells from cord blood	blood
14	chr3:112389000-112394000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr3:112389000-112394000	Enhancers	HSMM	muscle
16	chr3:112389200-112389600	ZNF genes & repeats	A549	lung
17	chr3:112389200-112390200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:112389200-112391600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:112389200-112391800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:112389200-112392000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:112389200-112392000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr3:112389200-112392200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr3:112389200-112396800	Enhancers	Osteobl	bone
24	chr3:112389400-112390000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:112389400-112390000	Bivalent Enhancer	GM12878-XiMat	blood
26	chr3:112389400-112390400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:112389400-112391600	Enhancers	NHEK	skin
28	chr3:112389400-112391800	Enhancers	Hela-S3	cervix
29	chr3:112389400-112392200	Enhancers	HMEC	breast
30	chr3:112389400-112392800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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