Variant report

Variant	rs13430254
Chromosome Location	chr2:72442093-72442094
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:72441964..72443908-chr2:72444024..72446667,3	MCF-7	breast:

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1000523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1003672	0.92[ASN][1000 genomes]
rs10175915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10178138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178847	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181899	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193543	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10204415	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs10205108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10209861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10221767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10221769	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10865390	0.92[ASN][1000 genomes]
rs11126362	0.85[ASN][1000 genomes]
rs11126363	0.92[ASN][1000 genomes]
rs1123199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1159763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1159764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1159765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1159766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11681809	0.92[ASN][1000 genomes]
rs12463825	0.90[EUR][1000 genomes]
rs12466026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12466112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13382986	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13387630	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391463	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs13392314	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13395204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13404369	0.92[ASN][1000 genomes]
rs13409641	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs13416674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13417114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13418637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13423761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13430651	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17673916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17724205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17724860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17725024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194235	1.00[CHB][hapmap]
rs194237	0.92[ASN][1000 genomes]
rs194238	0.92[ASN][1000 genomes]
rs194241	0.92[ASN][1000 genomes]
rs194242	0.85[ASN][1000 genomes]
rs194243	0.85[ASN][1000 genomes]
rs2041563	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2041564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2080044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109960	0.87[CEU][hapmap]
rs2109963	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2159823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28278	0.85[ASN][1000 genomes]
rs41386	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs41387	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41388	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41389	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41390	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41391	0.85[ASN][1000 genomes]
rs41392	1.00[CHB][hapmap]
rs41393	0.85[ASN][1000 genomes]
rs41394	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41396	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41398	0.85[ASN][1000 genomes]
rs41399	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs41400	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41401	1.00[CHB][hapmap]
rs41402	1.00[CHB][hapmap]
rs41403	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41405	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41406	1.00[CHB][hapmap]
rs41407	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41408	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs41409	0.80[CEU][hapmap];0.85[ASN][1000 genomes]
rs41415	0.88[CEU][hapmap];0.85[ASN][1000 genomes]
rs41416	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs41417	0.88[CEU][hapmap];0.85[ASN][1000 genomes]
rs41420	0.85[ASN][1000 genomes]
rs4852285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4852859	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852860	0.92[ASN][1000 genomes]
rs4852861	0.85[ASN][1000 genomes]
rs4852862	0.92[ASN][1000 genomes]
rs55764675	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55877105	0.85[ASN][1000 genomes]
rs55970539	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56045434	0.82[EUR][1000 genomes]
rs56143801	0.82[EUR][1000 genomes]
rs56299443	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147573	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147579	0.85[ASN][1000 genomes]
rs62147589	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147626	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147629	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147636	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62149273	0.89[EUR][1000 genomes]
rs6546752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6546753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6546755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6711257	0.81[EUR][1000 genomes]
rs6719255	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6751276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6760895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs719117	0.89[EUR][1000 genomes]
rs7565922	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs768042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs768043	0.85[ASN][1000 genomes]
rs9309463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][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	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13430254	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72432800-72456600	Weak transcription	Psoas Muscle	Psoas
2	chr2:72433000-72460600	Weak transcription	Pancreas	Pancrea
3	chr2:72433200-72442200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:72433200-72450000	Weak transcription	Brain Angular Gyrus	brain
5	chr2:72433200-72450000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:72433200-72466000	Weak transcription	Right Ventricle	heart
7	chr2:72433200-72468600	Weak transcription	Right Atrium	heart
8	chr2:72433400-72450200	Weak transcription	Brain Anterior Caudate	brain
9	chr2:72438200-72442200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:72438200-72446400	Weak transcription	Fetal Heart	heart
11	chr2:72438400-72449800	Weak transcription	HMEC	breast
12	chr2:72440400-72445200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:72441000-72462800	Weak transcription	Left Ventricle	heart
14	chr2:72441600-72442400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:72441600-72442400	Enhancers	Hela-S3	cervix
16	chr2:72441600-72442400	Enhancers	HepG2	liver
17	chr2:72441600-72442400	Enhancers	NH-A	brain
18	chr2:72441600-72442400	Enhancers	NHLF	lung
19	chr2:72441600-72442600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:72441600-72442600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr2:72441600-72442600	Enhancers	HUVEC	blood vessel
22	chr2:72441600-72442600	Enhancers	Osteobl	bone
23	chr2:72441600-72443400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:72441800-72442400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr2:72441800-72442400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:72441800-72442400	Enhancers	HSMMtube	muscle
27	chr2:72441800-72442400	Enhancers	NHDF-Ad	bronchial
28	chr2:72441800-72442600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:72441800-72442600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:72441800-72442600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:72441800-72442600	Flanking Active TSS	A549	lung
32	chr2:72442000-72442200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:72442000-72442400	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr2:72442000-72442400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr2:72442000-72442400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:72442000-72442400	Enhancers	Fetal Kidney	kidney
37	chr2:72442000-72442400	Enhancers	Fetal Stomach	stomach
38	chr2:72442000-72442800	Enhancers	Brain Substantia Nigra	brain

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