Variant report

Variant	rs4855836
Chromosome Location	chr3:49590256-49590257
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49588369..49590572-chr3:49704819..49707525,2	K562	blood:
2	chr3:49588932..49590951-chr3:49710802..49712975,2	K562	blood:
3	chr3:49582614..49585275-chr3:49588937..49591341,2	K562	blood:

Variant related genes	Relation type
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10212296	0.85[ASN][1000 genomes]
rs1050088	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865955	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130192	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130193	0.83[EUR][1000 genomes]
rs11130194	0.81[EUR][1000 genomes]
rs11130196	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130199	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130202	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130203	0.94[ASN][1000 genomes]
rs11130206	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11708955	0.82[ASN][1000 genomes]
rs11711485	0.82[ASN][1000 genomes]
rs11712569	0.94[ASN][1000 genomes]
rs11713474	0.86[ASN][1000 genomes]
rs11719996	0.94[ASN][1000 genomes]
rs11720264	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720458	0.92[ASN][1000 genomes]
rs11926781	0.86[ASN][1000 genomes]
rs12330269	0.94[ASN][1000 genomes]
rs12488065	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489092	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636099	0.83[ASN][1000 genomes]
rs13062429	0.83[ASN][1000 genomes]
rs13079082	0.94[ASN][1000 genomes]
rs13096760	0.84[EUR][1000 genomes]
rs1464566	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464567	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464568	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1568661	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1568662	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1801143	0.94[ASN][1000 genomes]
rs2312461	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34196454	0.90[ASN][1000 genomes]
rs34293138	0.94[ASN][1000 genomes]
rs34363169	0.94[ASN][1000 genomes]
rs34427167	0.86[ASN][1000 genomes]
rs35261698	0.94[ASN][1000 genomes]
rs35701831	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35999162	0.90[ASN][1000 genomes]
rs3811697	0.94[ASN][1000 genomes]
rs3870337	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870338	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3877784	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924462	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924463	0.91[EUR][1000 genomes]
rs3926569	0.90[ASN][1000 genomes]
rs4241406	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4241408	0.90[EUR][1000 genomes]
rs4459909	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4625	0.94[ASN][1000 genomes]
rs4855839	0.83[EUR][1000 genomes]
rs4855855	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4855859	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855861	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855864	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4855866	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4855873	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855877	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55957735	0.81[EUR][1000 genomes]
rs56116382	0.82[ASN][1000 genomes]
rs59152804	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62261185	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67216675	0.82[ASN][1000 genomes]
rs6766131	0.94[ASN][1000 genomes]
rs6766581	0.94[ASN][1000 genomes]
rs6784820	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6797664	0.94[ASN][1000 genomes]
rs71615484	0.90[ASN][1000 genomes]
rs7371895	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7622302	0.94[ASN][1000 genomes]
rs7630869	0.82[ASN][1000 genomes]
rs7633271	0.94[ASN][1000 genomes]
rs7637665	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7637999	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643586	0.81[EUR][1000 genomes]
rs7643845	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645445	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs885592	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9818590	0.94[ASN][1000 genomes]
rs9821311	0.84[ASN][1000 genomes]
rs9827021	0.94[ASN][1000 genomes]
rs9837027	0.94[ASN][1000 genomes]
rs9841110	0.82[ASN][1000 genomes]
rs9850072	0.94[ASN][1000 genomes]
rs9853683	0.94[ASN][1000 genomes]
rs9858280	0.90[ASN][1000 genomes]
rs9858418	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3369484	chr3:49586448-49590446	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4855836	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs4855836	WDR6	cis	Adipose Subcutaneous	GTEx
rs4855836	WDR6	cis	Nerve Tibial	GTEx
rs4855836	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs4855836	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs4855836	WDR6	cis	Artery Tibial	GTEx
rs4855836	WDR6	cis	Muscle Skeletal	GTEx
rs4855836	WDR6	cis	lung	GTEx
rs4855836	AMT	cis	Thyroid	GTEx
rs4855836	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49585200-49590600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:49585400-49590600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:49585800-49590400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:49586000-49590800	Weak transcription	Right Ventricle	heart
5	chr3:49587400-49590600	Enhancers	HepG2	liver
6	chr3:49587600-49590600	Weak transcription	Right Atrium	heart
7	chr3:49587800-49590600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:49588000-49590600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:49588200-49590400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:49588200-49590800	Weak transcription	HUVEC	blood vessel
11	chr3:49588200-49591000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:49588400-49590400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:49588400-49590600	Weak transcription	Adipose Nuclei	Adipose
14	chr3:49588600-49590400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:49588600-49590600	Weak transcription	Brain Substantia Nigra	brain
16	chr3:49588800-49591000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr3:49589000-49590400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:49589000-49591200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:49589200-49590600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:49589400-49590800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:49589400-49590800	Weak transcription	Fetal Intestine Large	intestine
22	chr3:49589400-49591200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr3:49589600-49590600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:49589600-49591200	Enhancers	Primary hematopoietic stem cells	blood
25	chr3:49589800-49590600	Enhancers	Dnd41	blood
26	chr3:49589800-49590800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:49589800-49591000	Enhancers	Lung	lung
28	chr3:49590200-49590800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:49590200-49590800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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