Variant report

Variant	rs6884704
Chromosome Location	chr5:112911800-112911801
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112910971..112913788-chr5:112914677..112918901,4	K562	blood:
2	chr5:112911409..112913819-chr5:112914953..112918122,3	K562	blood:

Variant related genes	Relation type
ENSG00000047188	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10039853	0.83[CEU][hapmap]
rs10040203	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs10046057	0.94[CEU][hapmap]
rs10053582	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs10061552	0.82[CEU][hapmap]
rs10071816	0.82[CEU][hapmap]
rs10079895	0.82[CEU][hapmap]
rs10079973	0.83[CEU][hapmap]
rs1017209	0.94[CEU][hapmap]
rs10477495	0.94[CEU][hapmap]
rs10477499	0.94[CEU][hapmap]
rs10477500	0.94[CEU][hapmap]
rs10478127	0.82[CEU][hapmap]
rs10478129	0.94[CEU][hapmap]
rs10478132	0.94[CEU][hapmap]
rs1052896	0.94[CEU][hapmap]
rs11241206	1.00[JPT][hapmap]
rs11241214	0.82[CEU][hapmap]
rs11241215	1.00[CEU][hapmap]
rs11738075	1.00[JPT][hapmap]
rs11738215	1.00[JPT][hapmap]
rs11747924	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11748145	0.85[ASN][1000 genomes]
rs11748794	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11749931	0.82[CEU][hapmap]
rs11956399	0.83[CEU][hapmap]
rs12186798	0.83[CEU][hapmap]
rs12519323	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]
rs12523255	1.00[JPT][hapmap]
rs12660001	0.82[CEU][hapmap]
rs13362066	0.94[CEU][hapmap]
rs17135597	1.00[JPT][hapmap]
rs17135608	1.00[JPT][hapmap]
rs17135616	1.00[JPT][hapmap]
rs17135630	1.00[JPT][hapmap]
rs17135753	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17135754	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1833678	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1833681	0.88[CEU][hapmap]
rs2042222	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2288449	0.82[CEU][hapmap]
rs2416281	0.84[ASN][1000 genomes]
rs2416319	0.82[EUR][1000 genomes]
rs2900072	0.82[EUR][1000 genomes]
rs3763138	0.94[CEU][hapmap]
rs3763140	0.83[CEU][hapmap]
rs3815911	0.81[CEU][hapmap]
rs3842917	0.82[CEU][hapmap]
rs3846721	1.00[JPT][hapmap]
rs3846722	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs3936061	0.82[CEU][hapmap]
rs4122546	0.82[ASN][1000 genomes]
rs4588592	0.83[CEU][hapmap]
rs4705551	0.88[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4705555	0.84[EUR][1000 genomes]
rs4705557	0.83[CEU][hapmap]
rs4705558	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4705817	1.00[JPT][hapmap]
rs4705819	1.00[JPT][hapmap]
rs4705823	0.94[CEU][hapmap]
rs4705825	0.94[CEU][hapmap]
rs4705826	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4705827	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs4705828	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs57077871	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6594721	0.94[CEU][hapmap]
rs6594732	0.94[CEU][hapmap]
rs6594733	0.94[CEU][hapmap]
rs6594734	0.82[CEU][hapmap]
rs67020702	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67723806	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6859688	0.85[ASN][1000 genomes]
rs6864369	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6864528	1.00[JPT][hapmap]
rs6865809	0.94[CEU][hapmap];0.84[JPT][hapmap]
rs6878001	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs6879800	1.00[JPT][hapmap]
rs6883383	0.82[CEU][hapmap]
rs6883441	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs6886628	0.82[CEU][hapmap]
rs6887816	0.94[CEU][hapmap]
rs6889574	0.82[CEU][hapmap]
rs6896469	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6896501	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6898425	0.87[CEU][hapmap]
rs72794121	0.88[ASN][1000 genomes]
rs73242809	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73247445	0.84[ASN][1000 genomes]
rs7702833	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7705562	0.83[CEU][hapmap]
rs7706958	0.82[CEU][hapmap]
rs7707443	0.93[CEU][hapmap];0.84[JPT][hapmap]
rs7711078	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7711211	0.88[CEU][hapmap]
rs7711367	0.82[CEU][hapmap]
rs7713038	0.94[CEU][hapmap]
rs7713451	0.94[CEU][hapmap]
rs7729306	0.94[CEU][hapmap]
rs7729433	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7730532	0.81[EUR][1000 genomes]
rs7730557	0.81[EUR][1000 genomes]
rs7730949	0.94[CEU][hapmap]
rs7737023	0.83[CEU][hapmap]
rs919304	0.82[CEU][hapmap]
rs929774	0.94[CEU][hapmap]
rs9326893	0.83[CEU][hapmap]
rs957777	0.88[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv520674	chr5:112911165-112942820	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking 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
rs6884704	YTHDC2	cis	multi-tissue	Pritchard
rs6884704	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112867400-112926000	Weak transcription	Small Intestine	intestine
2	chr5:112867400-112933000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:112870200-112930800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:112872000-112915000	Weak transcription	Hela-S3	cervix
5	chr5:112876000-112918800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:112889400-112930600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:112890600-112915800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:112891600-112912600	Weak transcription	Stomach Mucosa	stomach
9	chr5:112892800-112915000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:112894400-112911800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr5:112898200-112921200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:112899400-112929400	Weak transcription	HepG2	liver
13	chr5:112900400-112915800	Weak transcription	HUVEC	blood vessel
14	chr5:112901000-112911800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr5:112903000-112917000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr5:112904400-112917200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:112904600-112934800	Weak transcription	Psoas Muscle	Psoas
18	chr5:112904800-112916200	Weak transcription	Fetal Heart	heart
19	chr5:112907200-112915600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:112907400-112915600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr5:112907400-112932000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr5:112908800-112916000	Weak transcription	Fetal Brain Male	brain
23	chr5:112908800-112935200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr5:112909000-112911800	Strong transcription	Primary T cells from cord blood	blood
25	chr5:112909200-112912000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:112909400-112912200	Strong transcription	Liver	Liver
27	chr5:112909600-112915600	Weak transcription	Fetal Kidney	kidney
28	chr5:112910000-112911800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:112910200-112915600	Weak transcription	NHLF	lung
30	chr5:112910400-112915600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:112910400-112917200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr5:112910600-112912400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:112910600-112915200	Weak transcription	HSMM	muscle
34	chr5:112910600-112915200	Weak transcription	K562	blood
35	chr5:112910600-112915600	Weak transcription	Placenta	Placenta
36	chr5:112910600-112915800	Weak transcription	Brain Hippocampus Middle	brain
37	chr5:112910600-112915800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr5:112910600-112916400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:112910600-112917000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:112910600-112917000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr5:112910600-112917000	Weak transcription	Brain Angular Gyrus	brain
42	chr5:112910600-112919800	Weak transcription	NHDF-Ad	bronchial
43	chr5:112910600-112920000	Weak transcription	Brain Anterior Caudate	brain
44	chr5:112910600-112927000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:112910600-112927600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr5:112910600-112927800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr5:112910600-112933400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:112910600-112935200	Weak transcription	Spleen	Spleen
49	chr5:112910600-112935400	Weak transcription	Colon Smooth Muscle	Colon
50	chr5:112910600-112936600	Weak transcription	Colonic Mucosa	Colon

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