Variant report

Variant	rs41399
Chromosome Location	chr2:72420754-72420755
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:72411275..72413615-chr2:72420172..72422167,2	MCF-7	breast:
2	chr2:72420139..72423033-chr2:72428492..72430569,2	K562	blood:

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

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

rs_ID	r²[population]
rs1000523	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs1003672	0.85[ASN][1000 genomes]
rs10175915	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs10178138	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10178847	0.92[ASN][1000 genomes]
rs10181899	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10190799	0.86[ASN][1000 genomes]
rs10193543	0.92[ASN][1000 genomes]
rs10196589	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10205108	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10209861	1.00[CHB][hapmap]
rs10221767	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10221769	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10865390	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126362	0.93[ASN][1000 genomes]
rs11126363	0.85[ASN][1000 genomes]
rs1123199	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs1159763	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1159764	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1159765	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1159766	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs11681809	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12466026	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12466112	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13382986	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13387630	0.92[ASN][1000 genomes]
rs13389524	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13391463	1.00[CHB][hapmap]
rs13392314	0.92[ASN][1000 genomes]
rs13395204	1.00[CHB][hapmap]
rs13404369	0.85[ASN][1000 genomes]
rs13409641	0.83[CEU][hapmap]
rs13410366	1.00[YRI][hapmap]
rs13416674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13417114	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs13418637	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs13423761	1.00[CHB][hapmap]
rs13430254	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13430651	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17673916	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs17724205	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17724860	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs17725024	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs194235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs194236	0.81[ASN][1000 genomes]
rs194237	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194238	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194240	0.81[ASN][1000 genomes]
rs194241	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194242	0.93[ASN][1000 genomes]
rs194243	0.93[ASN][1000 genomes]
rs2041563	1.00[CHB][hapmap]
rs2041564	1.00[CHB][hapmap]
rs2080044	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2159823	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28278	0.93[ASN][1000 genomes]
rs41386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs41387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41389	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41390	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41391	0.93[ASN][1000 genomes]
rs41392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41393	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41395	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41397	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41398	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41400	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41401	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41405	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41407	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41409	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41410	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs41411	0.81[ASN][1000 genomes]
rs41412	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41413	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs41414	0.86[ASN][1000 genomes]
rs41415	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41416	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41417	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41418	0.86[ASN][1000 genomes]
rs41419	0.86[ASN][1000 genomes]
rs41420	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4852285	1.00[CHB][hapmap]
rs4852859	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4852860	0.85[ASN][1000 genomes]
rs4852862	0.85[ASN][1000 genomes]
rs55764675	0.92[ASN][1000 genomes]
rs55970539	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56299443	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62147573	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62147589	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62147626	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62147629	0.92[ASN][1000 genomes]
rs62147636	0.92[ASN][1000 genomes]
rs6546752	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs6546753	1.00[CHB][hapmap]
rs6546755	1.00[CHB][hapmap]
rs6719255	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs6748607	1.00[CHB][hapmap]
rs6751276	1.00[CHB][hapmap]
rs6760895	1.00[CHB][hapmap]
rs7565922	1.00[CHB][hapmap]
rs768042	1.00[CHB][hapmap]
rs9309463	1.00[CHB][hapmap];0.85[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
rs41399	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72406400-72425800	Weak transcription	Brain Anterior Caudate	brain
2	chr2:72407200-72425200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:72407800-72424600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:72409600-72426000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:72412800-72421600	Weak transcription	Gastric	stomach
6	chr2:72412800-72425400	Weak transcription	Stomach Mucosa	stomach
7	chr2:72412800-72429800	Weak transcription	Right Ventricle	heart
8	chr2:72412800-72431000	Weak transcription	Left Ventricle	heart
9	chr2:72415200-72426000	Weak transcription	NHEK	skin
10	chr2:72415400-72424400	Weak transcription	Aorta	Aorta
11	chr2:72415400-72426000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:72415400-72430800	Weak transcription	Placenta	Placenta
13	chr2:72419000-72430800	Weak transcription	Small Intestine	intestine
14	chr2:72419600-72429200	Weak transcription	Brain Substantia Nigra	brain
15	chr2:72420000-72425800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:72420400-72421200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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