Variant report

Variant	rs957777
Chromosome Location	chr5:112848654-112848655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr5:112848618-112849478	K562	blood:	n/a	n/a
2	WRNIP1	chr5:112848475-112848896	GM12878	blood:	n/a	n/a
3	RCOR1	chr5:112848211-112849835	IMR90	lung:	n/a	n/a
4	MXI1	chr5:112848600-112850607	SK-N-SH	brain:	n/a	n/a
5	STAT3	chr5:112848129-112848704	MCF10A-Er-Src	breast:	n/a	n/a
6	JUND	chr5:112848638-112850631	SK-N-SH	brain:	n/a	chr5:112849372-112849381
7	CTCF	chr5:112848414-112850388	A549	lung:	n/a	chr5:112850360-112850368
8	FOXA1	chr5:112848589-112848931	HepG2	liver:	n/a	n/a
9	CHD1	chr5:112848588-112850690	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112538594..112540259-chr5:112848065..112850694,2	MCF-7	breast:
2	chr5:112714356..112715276-chr5:112847595..112848868,4	MCF-7	breast:

Variant related genes	Relation type
YTHDC2	TF binding region
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10039853	0.94[CEU][hapmap]
rs10053582	0.81[CEU][hapmap]
rs10061552	0.94[CEU][hapmap]
rs10071816	0.94[CEU][hapmap]
rs10079895	0.94[CEU][hapmap]
rs10079973	0.94[CEU][hapmap]
rs10080096	0.89[CEU][hapmap]
rs10428666	1.00[JPT][hapmap]
rs10477497	0.88[CEU][hapmap]
rs10478127	0.94[CEU][hapmap]
rs10900685	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1116547	1.00[JPT][hapmap]
rs11241201	1.00[JPT][hapmap]
rs11241206	1.00[JPT][hapmap]
rs11241214	0.94[CEU][hapmap]
rs11241215	0.88[CEU][hapmap]
rs11738075	1.00[JPT][hapmap]
rs11738215	1.00[JPT][hapmap]
rs11747924	1.00[CEU][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11748145	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11748794	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11749931	0.94[CEU][hapmap]
rs11750945	0.82[CHB][hapmap]
rs11956399	0.94[CEU][hapmap]
rs12186798	0.94[CEU][hapmap]
rs12514091	1.00[JPT][hapmap]
rs12516418	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12519323	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12519818	0.82[ASN][1000 genomes]
rs12523255	1.00[JPT][hapmap]
rs12660001	0.94[CEU][hapmap]
rs1443683	1.00[JPT][hapmap]
rs17135597	1.00[JPT][hapmap]
rs17135608	1.00[JPT][hapmap]
rs17135616	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs17135630	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.85[ASN][1000 genomes]
rs17135753	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17135754	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1833678	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1850410	1.00[JPT][hapmap]
rs2042222	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2068923	1.00[JPT][hapmap]
rs2288449	0.94[CEU][hapmap]
rs2416281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763140	0.94[CEU][hapmap]
rs3815911	0.94[CEU][hapmap]
rs3846721	1.00[JPT][hapmap];0.92[YRI][hapmap]
rs3846722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3936061	0.94[CEU][hapmap]
rs4122546	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4334877	0.88[CEU][hapmap]
rs4588592	0.94[CEU][hapmap]
rs4705551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705557	0.94[CEU][hapmap]
rs4705558	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4705814	1.00[JPT][hapmap]
rs4705817	1.00[JPT][hapmap]
rs4705819	1.00[JPT][hapmap]
rs4705826	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57077871	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6594734	0.94[CEU][hapmap]
rs6594737	0.83[AMR][1000 genomes]
rs66490974	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66497221	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66502937	0.82[ASN][1000 genomes]
rs66583752	0.82[ASN][1000 genomes]
rs67020702	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67103739	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67268709	0.82[ASN][1000 genomes]
rs67723806	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6859688	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6861786	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6864369	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6864528	1.00[JPT][hapmap]
rs6877432	0.89[CEU][hapmap]
rs6877524	1.00[JPT][hapmap]
rs6878001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6879800	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs6882900	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6883383	0.94[CEU][hapmap]
rs6883441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6884704	0.88[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6886628	0.94[CEU][hapmap]
rs6889574	0.94[CEU][hapmap]
rs6896469	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6896501	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6898425	0.82[CEU][hapmap]
rs72792179	0.83[ASN][1000 genomes]
rs72794121	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72805465	0.84[EUR][1000 genomes]
rs73241779	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73242809	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73247445	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7349799	0.87[CEU][hapmap]
rs7702833	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7705562	0.94[CEU][hapmap]
rs7706958	0.94[CEU][hapmap]
rs7707443	1.00[CEU][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7711078	0.87[CEU][hapmap]
rs7711211	0.94[CEU][hapmap]
rs7711367	0.94[CEU][hapmap]
rs7717000	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7729433	0.82[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7737023	0.94[CEU][hapmap]
rs919304	0.94[CEU][hapmap]
rs9326893	0.94[CEU][hapmap]

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
rs957777	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL
rs957777	YTHDC2	cis	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112844800-112848800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr5:112845000-112848800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:112847200-112849000	Enhancers	Gastric	stomach
4	chr5:112847800-112848800	Enhancers	HepG2	liver
5	chr5:112847800-112849000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:112847800-112849000	Enhancers	HMEC	breast
7	chr5:112848000-112848800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:112848000-112848800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:112848000-112848800	Enhancers	NHEK	skin
10	chr5:112848400-112849000	Enhancers	Fetal Thymus	thymus
11	chr5:112848600-112848800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:112848600-112848800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr5:112848600-112848800	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr5:112848600-112848800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr5:112848600-112848800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:112848600-112848800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:112848600-112848800	Flanking Active TSS	Aorta	Aorta
18	chr5:112848600-112848800	Enhancers	Brain Anterior Caudate	brain
19	chr5:112848600-112848800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr5:112848600-112848800	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr5:112848600-112848800	Enhancers	NHDF-Ad	bronchial
22	chr5:112848600-112849000	Enhancers	H1 Cell Line	embryonic stem cell
23	chr5:112848600-112849000	Enhancers	Primary B cells from peripheral blood	blood
24	chr5:112848600-112849000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:112848600-112849000	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr5:112848600-112849000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr5:112848600-112849000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:112848600-112849000	Enhancers	Placenta Amnion	Placenta Amnion
29	chr5:112848600-112849000	Enhancers	Stomach Mucosa	stomach
30	chr5:112848600-112849200	Flanking Active TSS	GM12878-XiMat	blood
31	chr5:112848600-112849400	Flanking Active TSS	Dnd41	blood
32	chr5:112848600-112850000	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr5:112848600-112850200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:112848600-112850200	Active TSS	Colon Smooth Muscle	Colon
35	chr5:112848600-112850600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:112848600-112850600	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr5:112848600-112850800	Active TSS	K562	blood

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