Variant report

Variant	rs2416282
Chromosome Location	chr5:112848767-112848768
allele	G/T
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	POLR2A	chr5:112848702-112848769	ProgFib	skin:	n/a	n/a
2	KAP1	chr5:112848618-112849478	K562	blood:	n/a	n/a
3	ZNF263	chr5:112848757-112849639	HEK293-T-REx	kidney:	n/a	chr5:112849243-112849264
4	WRNIP1	chr5:112848475-112848896	GM12878	blood:	n/a	n/a
5	RCOR1	chr5:112848211-112849835	IMR90	lung:	n/a	n/a
6	USF2	chr5:112848765-112849513	Hela-S3	cervix:	n/a	chr5:112849331-112849347 chr5:112849332-112849348
7	MXI1	chr5:112848600-112850607	SK-N-SH	brain:	n/a	n/a
8	JUND	chr5:112848638-112850631	SK-N-SH	brain:	n/a	chr5:112849372-112849381
9	CTCF	chr5:112848414-112850388	A549	lung:	n/a	chr5:112850360-112850368
10	FOXA1	chr5:112848589-112848931	HepG2	liver:	n/a	n/a
11	CHD1	chr5:112848588-112850690	IMR90	lung:	n/a	n/a
12	SMC3	chr5:112848687-112849973	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:112538594..112540259-chr5:112848065..112850694,2	MCF-7	breast:
2	chr5:112714356..112715276-chr5:112847595..112848868,4	MCF-7	breast:
3	chr5:112823438..112825437-chr5:112848716..112850682,3	MCF-7	breast:

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

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1132528	0.84[ASW][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap]
rs12657961	0.82[ASW][hapmap]
rs1517210	0.84[ASW][hapmap];1.00[MKK][hapmap]
rs164251	0.80[AMR][1000 genomes]
rs164253	0.82[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs171181	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17327526	0.82[ASW][hapmap];1.00[LWK][hapmap]
rs182987	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs190453	0.80[AMR][1000 genomes]
rs2431548	0.82[AMR][1000 genomes]
rs2434664	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2434665	0.80[AMR][1000 genomes]
rs255856	0.84[ASW][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap]
rs26983	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs27566	0.84[ASW][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap]
rs27700	0.80[AMR][1000 genomes]
rs2914153	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2914252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348927	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs348933	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs348937	0.83[GIH][hapmap]
rs348949	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs348950	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs348953	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs348959	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs368352	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857435	0.84[ASW][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap]
rs3906371	0.88[MEX][hapmap]
rs406288	0.81[AMR][1000 genomes]
rs423089	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs459428	0.82[AMR][1000 genomes]
rs463216	0.81[AMR][1000 genomes]
rs4639215	0.84[ASW][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap]
rs465898	0.82[AMR][1000 genomes]
rs675353	0.84[ASW][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7727449	0.80[MEX][hapmap]
rs9326895	0.84[ASW][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap]
rs9552	0.82[ASW][hapmap];0.88[MEX][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
rs2416282	YTHDC2	cis	parietal	SCAN
rs2416282	YTHDC2	cis	cerebellum	SCAN

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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