Variant report

Variant	rs12519323
Chromosome Location	chr5:112894805-112894806
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10039853	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs10053582	0.81[CEU][hapmap]
rs10061552	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs10071816	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs10079758	0.83[EUR][1000 genomes]
rs10079895	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs10079973	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs10080096	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs10477497	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs10477498	0.81[EUR][1000 genomes]
rs10478127	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs10900685	1.00[JPT][hapmap]
rs11241206	0.88[JPT][hapmap]
rs11241214	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs11241215	0.88[CEU][hapmap]
rs11738075	0.88[JPT][hapmap]
rs11738215	0.88[JPT][hapmap]
rs11747924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11748145	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11748794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11749931	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs11750945	0.89[JPT][hapmap]
rs11956399	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs12186798	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs12516418	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12523255	0.85[JPT][hapmap]
rs12652172	0.84[EUR][1000 genomes]
rs12654189	0.81[EUR][1000 genomes]
rs12660001	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs17135597	0.86[JPT][hapmap]
rs17135608	0.86[JPT][hapmap]
rs17135616	0.88[JPT][hapmap];0.87[YRI][hapmap]
rs17135630	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs17135753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17135754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1833678	1.00[CEU][hapmap];1.00[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];0.92[ASN][1000 genomes]
rs2042222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2162842	0.83[EUR][1000 genomes]
rs2288449	0.94[CEU][hapmap]
rs2416281	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28558374	0.83[EUR][1000 genomes]
rs34514665	0.81[EUR][1000 genomes]
rs34864074	0.81[EUR][1000 genomes]
rs35162738	0.81[EUR][1000 genomes]
rs3763140	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs3815911	0.94[CEU][hapmap]
rs3846721	0.88[JPT][hapmap];0.92[YRI][hapmap]
rs3846722	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3936061	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs4122546	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4334877	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs4588592	0.94[CEU][hapmap]
rs4705551	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4705553	0.81[EUR][1000 genomes]
rs4705557	0.94[CEU][hapmap]
rs4705558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4705814	0.88[JPT][hapmap]
rs4705817	0.86[JPT][hapmap]
rs4705819	0.85[JPT][hapmap]
rs4705826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57077871	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58044020	0.83[EUR][1000 genomes]
rs60871281	0.82[EUR][1000 genomes]
rs6594734	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs6594737	0.81[AMR][1000 genomes]
rs66490974	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66497221	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67020702	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67103739	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67723806	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6859688	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6861786	0.81[EUR][1000 genomes]
rs6864369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6864528	0.88[JPT][hapmap]
rs6877432	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs6878001	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6879800	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs6882900	0.81[EUR][1000 genomes]
rs6883383	0.94[CEU][hapmap]
rs6883441	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6884704	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6886628	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs6889501	0.83[EUR][1000 genomes]
rs6889574	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs6896469	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6896501	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6898425	0.82[CEU][hapmap]
rs72794121	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72805422	0.83[EUR][1000 genomes]
rs73241779	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73242809	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73247445	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7349799	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs7702833	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7705562	0.94[CEU][hapmap]
rs7706215	0.83[EUR][1000 genomes]
rs7706958	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs7707443	1.00[CEU][hapmap];0.84[YRI][hapmap];0.85[EUR][1000 genomes]
rs7711078	0.87[CEU][hapmap]
rs7711211	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs7711367	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs7717000	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7729433	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7737023	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs919304	0.94[CEU][hapmap]
rs9326893	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs957777	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]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv882722	chr5:112868878-112899573	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
rs12519323	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL
rs12519323	YTHDC2	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112850400-112904000	Weak transcription	Psoas Muscle	Psoas
2	chr5:112850600-112908400	Weak transcription	Colonic Mucosa	Colon
3	chr5:112851600-112902800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:112867000-112910000	Weak transcription	Right Ventricle	heart
5	chr5:112867200-112903400	Weak transcription	Pancreas	Pancrea
6	chr5:112867200-112904000	Weak transcription	Lung	lung
7	chr5:112867200-112904200	Weak transcription	Aorta	Aorta
8	chr5:112867200-112909800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:112867200-112909800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:112867200-112910000	Weak transcription	Esophagus	oesophagus
11	chr5:112867400-112926000	Weak transcription	Small Intestine	intestine
12	chr5:112867400-112933000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:112868600-112911400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr5:112869200-112910000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:112870200-112930800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:112872000-112904000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:112872000-112915000	Weak transcription	Hela-S3	cervix
18	chr5:112873000-112900600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr5:112873400-112908800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:112874000-112909600	Weak transcription	Spleen	Spleen
21	chr5:112874400-112902600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:112876000-112918800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:112877200-112905800	Weak transcription	Fetal Stomach	stomach
24	chr5:112879600-112895200	Weak transcription	Left Ventricle	heart
25	chr5:112879600-112902800	Weak transcription	Thymus	Thymus
26	chr5:112879600-112904200	Weak transcription	Gastric	stomach
27	chr5:112881800-112906400	Weak transcription	Fetal Intestine Small	intestine
28	chr5:112882600-112904000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr5:112882800-112909600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:112883000-112899600	Weak transcription	Brain Angular Gyrus	brain
31	chr5:112883000-112903200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:112883200-112895200	Weak transcription	NHEK	skin
33	chr5:112883200-112896400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:112883400-112895400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:112883800-112907400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:112884200-112905200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:112884200-112905600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:112884200-112908000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:112884800-112896800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:112885400-112895000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr5:112885400-112897800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr5:112885600-112895000	Weak transcription	A549	lung
43	chr5:112885800-112896000	Weak transcription	K562	blood
44	chr5:112886000-112895000	Weak transcription	Colon Smooth Muscle	Colon
45	chr5:112886000-112902400	Weak transcription	NHLF	lung
46	chr5:112886600-112911200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr5:112887800-112904400	Strong transcription	Fetal Intestine Large	intestine
48	chr5:112888000-112908200	Strong transcription	Liver	Liver
49	chr5:112888600-112898000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:112888600-112901400	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links