Variant report

Variant	rs13417114
Chromosome Location	chr2:72433296-72433297
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	chr2:72431398..72433535-chr2:72436487..72438674,2	MCF-7	breast:
2	chr2:72432812..72434707-chr2:72436307..72438652,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1000523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1003672	0.85[ASN][1000 genomes]
rs10175915	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs10178138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10178847	0.92[ASN][1000 genomes]
rs10181899	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10190799	0.86[ASN][1000 genomes]
rs10193543	0.92[ASN][1000 genomes]
rs10196589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10204415	0.87[GIH][hapmap]
rs10205108	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10209861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10221767	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10221769	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10490040	0.81[YRI][hapmap]
rs10865390	0.85[ASN][1000 genomes]
rs11126363	0.85[ASN][1000 genomes]
rs1123199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1159763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1159764	1.00[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1159765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1159766	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11681809	0.85[ASN][1000 genomes]
rs12466026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12466112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13382986	0.92[ASN][1000 genomes]
rs13387630	0.92[ASN][1000 genomes]
rs13389524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13391463	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs13392314	0.92[ASN][1000 genomes]
rs13395204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13403438	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13404369	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416674	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]
rs13418637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13423761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13430254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13430651	0.92[ASN][1000 genomes]
rs13432350	0.83[GIH][hapmap]
rs17673916	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs17724205	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17724860	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs17725024	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs194235	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[ASN][1000 genomes]
rs194237	0.85[ASN][1000 genomes]
rs194238	0.85[ASN][1000 genomes]
rs194241	0.85[ASN][1000 genomes]
rs2041563	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2041564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2080044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2109963	1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2159823	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2192015	0.88[GIH][hapmap]
rs41386	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap]
rs41387	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41388	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs41389	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs41390	1.00[CHB][hapmap]
rs41392	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs41393	1.00[CHD][hapmap];0.87[GIH][hapmap]
rs41394	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs41395	0.86[ASN][1000 genomes]
rs41396	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs41398	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs41399	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41400	1.00[CHB][hapmap]
rs41401	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[ASN][1000 genomes]
rs41402	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[ASN][1000 genomes]
rs41403	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs41405	1.00[CHB][hapmap]
rs41406	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs41407	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs41408	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs41410	0.81[ASN][1000 genomes]
rs41411	0.81[ASN][1000 genomes]
rs41412	0.83[GIH][hapmap]
rs41413	0.87[GIH][hapmap];0.81[ASN][1000 genomes]
rs41415	0.87[GIH][hapmap]
rs41416	0.87[GIH][hapmap]
rs41417	0.91[GIH][hapmap]
rs4852285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4852286	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs4852288	0.83[GIH][hapmap]
rs4852859	0.92[ASN][1000 genomes]
rs4852860	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852861	0.93[ASN][1000 genomes]
rs4852862	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55764675	0.92[ASN][1000 genomes]
rs55877105	0.93[ASN][1000 genomes]
rs55970539	0.92[ASN][1000 genomes]
rs56299443	0.92[ASN][1000 genomes]
rs62147573	0.92[ASN][1000 genomes]
rs62147579	0.93[ASN][1000 genomes]
rs62147589	0.92[ASN][1000 genomes]
rs62147626	0.92[ASN][1000 genomes]
rs62147629	0.92[ASN][1000 genomes]
rs62147636	0.92[ASN][1000 genomes]
rs6546750	0.81[ASN][1000 genomes]
rs6546752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6546753	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6546755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6719255	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6748607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6751276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6760895	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7559131	0.83[GIH][hapmap]
rs7565922	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7583271	0.83[GIH][hapmap]
rs768042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs768043	0.93[ASN][1000 genomes]
rs9309463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9679148	0.81[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13417114	MPHOSPH10	cis	cerebellum	SCAN
rs13417114	BOLA3	cis	parietal	SCAN
rs13417114	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72426800-72437600	Weak transcription	NH-A	brain
2	chr2:72429200-72433600	Enhancers	Fetal Intestine Large	intestine
3	chr2:72430200-72433400	Enhancers	Brain Substantia Nigra	brain
4	chr2:72430400-72433600	Enhancers	Fetal Stomach	stomach
5	chr2:72430600-72433400	Enhancers	Brain Anterior Caudate	brain
6	chr2:72430800-72433400	Enhancers	Fetal Intestine Small	intestine
7	chr2:72430800-72433600	Enhancers	Duodenum Mucosa	Duodenum
8	chr2:72430800-72433600	Enhancers	Small Intestine	intestine
9	chr2:72431000-72433600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:72431200-72433400	Enhancers	Fetal Heart	heart
11	chr2:72431200-72433400	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr2:72431400-72433800	Enhancers	Brain Hippocampus Middle	brain
13	chr2:72432200-72433800	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr2:72432800-72437600	Weak transcription	Colonic Mucosa	Colon
15	chr2:72432800-72437600	Weak transcription	Esophagus	oesophagus
16	chr2:72432800-72437600	Weak transcription	Gastric	stomach
17	chr2:72432800-72437800	Weak transcription	Osteobl	bone
18	chr2:72432800-72438400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:72432800-72438400	Weak transcription	NHDF-Ad	bronchial
20	chr2:72432800-72441600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:72432800-72456600	Weak transcription	Psoas Muscle	Psoas
22	chr2:72433000-72433600	Enhancers	HepG2	liver
23	chr2:72433000-72441600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:72433000-72460600	Weak transcription	Pancreas	Pancrea
25	chr2:72433200-72436600	Weak transcription	A549	lung
26	chr2:72433200-72437600	Weak transcription	Stomach Mucosa	stomach
27	chr2:72433200-72437800	Weak transcription	Ovary	ovary
28	chr2:72433200-72438600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:72433200-72440200	Weak transcription	Left Ventricle	heart
30	chr2:72433200-72442200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:72433200-72450000	Weak transcription	Brain Angular Gyrus	brain
32	chr2:72433200-72450000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:72433200-72466000	Weak transcription	Right Ventricle	heart
34	chr2:72433200-72468600	Weak transcription	Right Atrium	heart

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