Variant report

Variant	rs4062889
Chromosome Location	chr5:70864554-70864555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10044572	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10055460	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10060578	0.85[EUR][1000 genomes]
rs10064099	0.87[EUR][1000 genomes]
rs10077085	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10434642	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10474383	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10805884	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10942284	0.85[EUR][1000 genomes]
rs10942533	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10942682	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10942700	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10942702	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10942705	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11743135	0.89[EUR][1000 genomes]
rs11746722	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12152748	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12153571	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12514732	0.89[EUR][1000 genomes]
rs12516456	0.85[EUR][1000 genomes]
rs12652715	0.86[AMR][1000 genomes]
rs13157835	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3748043	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4505929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5005863	0.82[EUR][1000 genomes]
rs62361818	0.86[AMR][1000 genomes]
rs6452722	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6452900	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453013	0.83[EUR][1000 genomes]
rs6453014	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6453018	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6453035	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6453043	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6872235	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6872671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6877289	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6877773	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6886336	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6898471	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs715747	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7378662	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7380115	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7380280	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7444322	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7447726	0.85[EUR][1000 genomes]
rs7448422	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7449316	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7714527	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7715648	0.85[EUR][1000 genomes]
rs7721179	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7727576	0.85[EUR][1000 genomes]
rs7728577	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7735544	0.83[EUR][1000 genomes]
rs9968768	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv2754424	chr5:70749744-70885544	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4062889	MCCC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70778400-70869600	Weak transcription	Stomach Mucosa	stomach
2	chr5:70825800-70869200	Weak transcription	Fetal Heart	heart
3	chr5:70831400-70864600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr5:70834000-70871800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:70839400-70870000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:70846000-70872800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:70846200-70866200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:70846200-70867600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:70847400-70864600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:70847600-70869800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:70848400-70864800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:70848600-70865000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:70848600-70865000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr5:70848800-70864800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:70848800-70864800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:70848800-70865200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:70849800-70866000	Weak transcription	Colonic Mucosa	Colon
18	chr5:70850000-70882200	Weak transcription	Psoas Muscle	Psoas
19	chr5:70854200-70866000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr5:70856800-70866000	Weak transcription	Fetal Brain Male	brain
21	chr5:70856800-70882400	Weak transcription	NHEK	skin
22	chr5:70857000-70882200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:70857800-70882200	Weak transcription	Brain Angular Gyrus	brain
24	chr5:70858600-70873800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:70858800-70869600	Weak transcription	HepG2	liver
26	chr5:70858800-70882200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr5:70858800-70882200	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:70859200-70865800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:70859200-70869600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr5:70859200-70872400	Weak transcription	Ovary	ovary
31	chr5:70859200-70882400	Weak transcription	Right Ventricle	heart
32	chr5:70859400-70866600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:70859400-70866600	Weak transcription	Hela-S3	cervix
34	chr5:70859400-70869600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:70859400-70882200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:70860400-70864600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:70860400-70864800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:70860600-70865000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:70861400-70882200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr5:70861400-70882400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr5:70861600-70865800	Weak transcription	NHLF	lung
42	chr5:70861600-70866200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr5:70861600-70867400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr5:70861600-70868200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr5:70861600-70869400	Weak transcription	K562	blood
46	chr5:70861600-70870000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr5:70861600-70882200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr5:70861600-70882200	Weak transcription	GM12878-XiMat	blood
49	chr5:70861600-70882400	Weak transcription	Primary B cells from cord blood	blood
50	chr5:70863200-70864600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links