Variant report

Variant	rs12523145
Chromosome Location	chr5:112852568-112852569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112851058..112853151-chr5:112859618..112861901,3	MCF-7	breast:
2	chr5:112851205..112853122-chr5:112875699..112878060,2	K562	blood:
3	chr5:112823583..112825426-chr5:112850163..112852982,2	MCF-7	breast:
4	chr5:112781329..112783390-chr5:112851064..112853901,2	K562	blood:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10036300	0.85[CHB][hapmap]
rs10039853	0.92[CHB][hapmap]
rs10040203	0.93[CHB][hapmap]
rs10046057	0.86[CHB][hapmap]
rs10061552	0.93[CHB][hapmap]
rs10071816	0.86[CHB][hapmap]
rs10079603	0.86[CHB][hapmap]
rs10079895	0.92[CHB][hapmap]
rs10079973	0.93[CHB][hapmap]
rs10080096	0.93[CHB][hapmap]
rs1017209	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes]
rs10477495	0.86[CHB][hapmap]
rs10477497	0.93[CHB][hapmap]
rs10477499	0.92[CHB][hapmap]
rs10477500	0.93[CHB][hapmap]
rs10478127	0.92[CHB][hapmap]
rs10478129	0.93[CHB][hapmap]
rs10478132	0.93[CHB][hapmap]
rs1052896	0.91[CHB][hapmap]
rs11241211	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11241212	0.89[AMR][1000 genomes]
rs11241214	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs11241215	0.91[CHB][hapmap]
rs11749931	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs11956399	0.93[CHB][hapmap]
rs12186798	0.93[CHB][hapmap]
rs12519315	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12659978	0.82[JPT][hapmap]
rs12660001	0.92[CHB][hapmap]
rs13362066	0.86[CHB][hapmap];0.80[AMR][1000 genomes]
rs1820056	0.82[JPT][hapmap]
rs1820059	0.89[AMR][1000 genomes]
rs1833680	0.86[AMR][1000 genomes]
rs1833681	0.93[CHB][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes]
rs1862315	0.86[AMR][1000 genomes]
rs1970798	0.89[AMR][1000 genomes]
rs2288449	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs2416319	0.80[AMR][1000 genomes]
rs255879	0.82[AMR][1000 genomes]
rs26991	0.96[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2910018	0.87[JPT][hapmap]
rs3763138	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs3763140	0.93[CHB][hapmap]
rs3815911	0.91[CHD][hapmap]
rs3906538	0.83[AMR][1000 genomes]
rs3909887	0.83[AMR][1000 genomes]
rs3936061	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs4122547	0.81[AMR][1000 genomes]
rs4334877	0.93[CHB][hapmap]
rs4415069	0.82[JPT][hapmap]
rs4639215	0.82[JPT][hapmap]
rs4705557	0.93[CHB][hapmap]
rs4705825	0.86[CHB][hapmap];0.88[CHD][hapmap];0.92[MEX][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes]
rs4705827	0.86[CHB][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap]
rs4705828	1.00[CHB][hapmap]
rs4705830	0.82[JPT][hapmap]
rs60265545	0.83[AMR][1000 genomes]
rs6594721	0.86[CHB][hapmap];0.88[CHD][hapmap];0.84[MEX][hapmap]
rs6594732	0.86[CHB][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap]
rs6594733	0.86[CHB][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap]
rs6594734	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs6594735	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs67915940	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6877432	0.93[CHB][hapmap];0.90[CHD][hapmap]
rs6878355	0.86[AMR][1000 genomes]
rs6881976	0.82[JPT][hapmap]
rs6883383	0.93[CHB][hapmap]
rs6886199	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[ASN][1000 genomes]
rs6886628	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs6887816	0.86[CHB][hapmap]
rs6889574	0.93[CHB][hapmap];0.90[CHD][hapmap]
rs6889783	0.83[AMR][1000 genomes]
rs6898425	0.86[CHB][hapmap]
rs7349799	0.92[CHB][hapmap]
rs7701913	0.86[AMR][1000 genomes]
rs7705562	0.93[CHB][hapmap]
rs7706958	0.93[CHB][hapmap]
rs7711078	0.91[CHB][hapmap]
rs7711211	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs7711367	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs7713038	0.93[CHB][hapmap]
rs7713451	0.93[CHB][hapmap];0.90[CHD][hapmap];0.84[MEX][hapmap]
rs7713846	0.86[AMR][1000 genomes]
rs7717644	0.86[AMR][1000 genomes]
rs7729306	0.93[CHB][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap]
rs7730949	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs7732310	0.80[AMR][1000 genomes]
rs7737023	0.93[CHB][hapmap]
rs8180416	0.94[YRI][hapmap]
rs919304	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs929774	0.86[CHB][hapmap];0.86[AMR][1000 genomes]
rs9326890	0.80[LWK][hapmap];0.94[YRI][hapmap]
rs9326891	0.93[YRI][hapmap]
rs9326893	0.93[CHB][hapmap]
rs9326895	0.82[JPT][hapmap]
rs9654519	0.89[AMR][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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12523145	CDO1	cis	cerebellum	SCAN
rs12523145	YTHDC2	cis	cerebellum	SCAN
rs12523145	YTHDC2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112850400-112852800	Weak transcription	Fetal Lung	lung
2	chr5:112850400-112853000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:112850400-112853000	Weak transcription	HSMM	muscle
4	chr5:112850400-112853200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr5:112850400-112853200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:112850400-112853400	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr5:112850400-112855600	Weak transcription	Left Ventricle	heart
8	chr5:112850400-112856000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:112850400-112856200	Weak transcription	Ovary	ovary
10	chr5:112850400-112856200	Weak transcription	Thymus	Thymus
11	chr5:112850400-112857800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:112850400-112858200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:112850400-112863600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:112850400-112866600	Weak transcription	Esophagus	oesophagus
15	chr5:112850400-112866600	Weak transcription	Placenta	Placenta
16	chr5:112850400-112866800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:112850400-112866800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:112850400-112866800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr5:112850400-112866800	Weak transcription	Aorta	Aorta
20	chr5:112850400-112866800	Weak transcription	Lung	lung
21	chr5:112850400-112867000	Weak transcription	Pancreas	Pancrea
22	chr5:112850400-112879000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:112850400-112879200	Weak transcription	Gastric	stomach
24	chr5:112850400-112904000	Weak transcription	Psoas Muscle	Psoas
25	chr5:112850600-112852600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:112850600-112852800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr5:112850600-112852800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:112850600-112852800	Weak transcription	Fetal Intestine Large	intestine
29	chr5:112850600-112853000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:112850600-112853400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:112850600-112853800	Weak transcription	Fetal Stomach	stomach
32	chr5:112850600-112855200	Weak transcription	Right Ventricle	heart
33	chr5:112850600-112857600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr5:112850600-112860600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr5:112850600-112862000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:112850600-112865400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr5:112850600-112865600	Weak transcription	Fetal Kidney	kidney
38	chr5:112850600-112866600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr5:112850600-112866600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr5:112850600-112867600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:112850600-112868600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:112850600-112874800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr5:112850600-112879200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:112850600-112908400	Weak transcription	Colonic Mucosa	Colon
45	chr5:112850800-112852600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:112850800-112853000	Weak transcription	Primary T cells from cord blood	blood
47	chr5:112850800-112853600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr5:112850800-112853800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:112850800-112854200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:112850800-112856200	Weak transcription	NHDF-Ad	bronchial

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