Variant report

Variant	rs6896501
Chromosome Location	chr5:112906601-112906602
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10038632	0.82[EUR][1000 genomes]
rs10063008	0.80[EUR][1000 genomes]
rs11747924	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11748145	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11748794	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12519323	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13359703	0.80[EUR][1000 genomes]
rs17135753	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17135754	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1833678	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2042222	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2416281	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3846722	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4122546	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4588592	0.82[EUR][1000 genomes]
rs4705551	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705558	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705826	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57077871	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60914066	0.80[EUR][1000 genomes]
rs6594737	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs66490974	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66497221	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67020702	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67103739	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67723806	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6859688	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6861786	0.82[EUR][1000 genomes]
rs6864369	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6867502	0.82[EUR][1000 genomes]
rs6877466	0.82[EUR][1000 genomes]
rs6877834	0.80[EUR][1000 genomes]
rs6878001	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6882900	0.82[EUR][1000 genomes]
rs6883441	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6884704	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6896469	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72794121	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72805465	0.88[EUR][1000 genomes]
rs73241779	0.87[EUR][1000 genomes]
rs73242809	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73247445	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7702833	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7707443	0.86[EUR][1000 genomes]
rs7722918	0.82[EUR][1000 genomes]
rs7729433	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs957777	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882720	chr5:112859994-112911165	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv882721	chr5:112859994-112963488	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv882723	chr5:112868878-112911165	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv882724	chr5:112868878-112933202	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1033202	chr5:112891857-112945992	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6896501	YTHDC2	cis	multi-tissue	Pritchard
rs6896501	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112850600-112908400	Weak transcription	Colonic Mucosa	Colon
2	chr5:112867000-112910000	Weak transcription	Right Ventricle	heart
3	chr5:112867200-112909800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:112867200-112909800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:112867200-112910000	Weak transcription	Esophagus	oesophagus
6	chr5:112867400-112926000	Weak transcription	Small Intestine	intestine
7	chr5:112867400-112933000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:112868600-112911400	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr5:112869200-112910000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:112870200-112930800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:112872000-112915000	Weak transcription	Hela-S3	cervix
12	chr5:112873400-112908800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:112874000-112909600	Weak transcription	Spleen	Spleen
14	chr5:112876000-112918800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:112882800-112909600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:112883800-112907400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:112884200-112908000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:112886600-112911200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr5:112888000-112908200	Strong transcription	Liver	Liver
20	chr5:112888800-112908400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:112889400-112930600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:112889800-112909600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr5:112889800-112910000	Weak transcription	HSMMtube	muscle
24	chr5:112890600-112915800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:112891600-112908200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:112891600-112912600	Weak transcription	Stomach Mucosa	stomach
27	chr5:112892800-112915000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:112894400-112911800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr5:112894600-112910800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:112894800-112907400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr5:112894800-112908000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr5:112895000-112911400	Strong transcription	Dnd41	blood
33	chr5:112896000-112908400	Weak transcription	Brain Hippocampus Middle	brain
34	chr5:112896800-112909800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:112896800-112909800	Weak transcription	NHEK	skin
36	chr5:112898000-112909000	Weak transcription	Colon Smooth Muscle	Colon
37	chr5:112898200-112921200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr5:112898400-112909600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:112898600-112909800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:112899400-112929400	Weak transcription	HepG2	liver
41	chr5:112899800-112909800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr5:112900400-112915800	Weak transcription	HUVEC	blood vessel
43	chr5:112901000-112906800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:112901000-112911000	Strong transcription	Fetal Lung	lung
45	chr5:112901000-112911800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr5:112901200-112907600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr5:112901200-112909000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr5:112901400-112907600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr5:112901400-112910800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:112901400-112911600	Strong transcription	Adipose Nuclei	Adipose

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