Variant report

Variant	rs6878355
Chromosome Location	chr5:112852624-112852625
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: 170 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:169)

rs_ID	r²[population]
rs10036298	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10036300	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10038632	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10039853	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10040203	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10040430	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10040516	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10042563	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10043066	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10046057	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10052077	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10053582	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10061552	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10063008	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10065616	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10071816	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10072547	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10076131	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10079603	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10079758	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10079895	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10079973	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10080096	0.93[ASN][1000 genomes]
rs1017209	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1035888	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10477495	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10477497	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10477498	0.93[ASN][1000 genomes]
rs10477499	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10477500	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10478126	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10478127	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10478129	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10478132	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1052896	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1080858	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11241210	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11241211	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11241212	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11241214	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11241215	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11742968	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11749931	0.93[ASN][1000 genomes]
rs11750449	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11750488	0.86[EUR][1000 genomes]
rs11956399	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12186798	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12514105	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12516911	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12519315	0.81[AMR][1000 genomes]
rs12523145	0.86[AMR][1000 genomes]
rs12652172	0.93[ASN][1000 genomes]
rs12654189	0.93[ASN][1000 genomes]
rs12660001	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13359625	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13359648	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13359652	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13359703	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13362066	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1549628	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17135766	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17135776	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1820059	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1833680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1833681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1862315	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1970798	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2115216	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2162842	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2162847	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2288449	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2416319	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28558374	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28848005	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2900072	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34514665	0.96[ASN][1000 genomes]
rs34864074	0.96[ASN][1000 genomes]
rs35162738	0.96[ASN][1000 genomes]
rs35526509	0.92[ASN][1000 genomes]
rs3763138	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3763140	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3815911	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3842917	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3906538	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3909887	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3936061	0.96[ASN][1000 genomes]
rs4122547	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4132093	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4132094	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4334877	0.96[ASN][1000 genomes]
rs4588592	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4705552	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705553	0.95[ASN][1000 genomes]
rs4705555	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4705556	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4705557	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4705823	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4705825	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705827	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705828	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705832	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4705833	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56030143	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56206672	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57134656	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58044020	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58391392	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60265545	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60871281	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60914066	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6594718	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6594719	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6594720	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6594721	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6594729	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6594732	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6594733	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6594734	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6594738	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67915940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6865809	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6867502	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6876448	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6877432	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6877466	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6877834	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6878282	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6878900	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6880447	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6883383	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6883557	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6886628	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6887816	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6889501	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6889574	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6889783	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6898425	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72805422	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7349799	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs754573	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7701913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7704170	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7706215	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7706796	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7706958	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7707895	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7709110	0.81[ASN][1000 genomes]
rs7711078	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7711211	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7711367	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7713038	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7713451	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7713846	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7715601	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7717644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7722918	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7723108	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7729306	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7730532	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7730557	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7730949	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7732310	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7737023	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs919304	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs929774	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9326893	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9326897	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9654519	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9885245	0.87[AMR][1000 genomes];0.88[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6878355	YTHDC2	cis	multi-tissue	Pritchard
rs6878355	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL

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	chr5:112850600-112852800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr5:112850600-112852800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:112850600-112852800	Weak transcription	Fetal Intestine Large	intestine
28	chr5:112850600-112853000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr5:112850600-112853400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr5:112850600-112853800	Weak transcription	Fetal Stomach	stomach
31	chr5:112850600-112855200	Weak transcription	Right Ventricle	heart
32	chr5:112850600-112857600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:112850600-112860600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr5:112850600-112862000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr5:112850600-112865400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr5:112850600-112865600	Weak transcription	Fetal Kidney	kidney
37	chr5:112850600-112866600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:112850600-112866600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr5:112850600-112867600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr5:112850600-112868600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr5:112850600-112874800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr5:112850600-112879200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:112850600-112908400	Weak transcription	Colonic Mucosa	Colon
44	chr5:112850800-112853000	Weak transcription	Primary T cells from cord blood	blood
45	chr5:112850800-112853600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:112850800-112853800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:112850800-112854200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:112850800-112856200	Weak transcription	NHDF-Ad	bronchial
49	chr5:112850800-112856400	Weak transcription	Brain Germinal Matrix	brain
50	chr5:112851200-112852800	Enhancers	Duodenum Smooth Muscle	Duodenum

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