Variant report

Variant	rs3002285
Chromosome Location	chr1:213182137-213182138
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:213181670..213183610-chr1:213239106..213241816,2	K562	blood:
2	chr1:213180453..213182672-chr1:213253594..213256441,2	K562	blood:
3	chr1:213175599..213177559-chr1:213181937..213184219,2	K562	blood:
4	chr1:213180724..213183170-chr1:213240316..213242506,2	K562	blood:
5	chr1:213164117..213166257-chr1:213181504..213183921,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10465694	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10864034	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1566247	0.81[AMR][1000 genomes]
rs1976333	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1995151	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap]
rs2132428	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2172982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2935209	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2935219	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936010	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2936011	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3002284	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs3010779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3010780	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3010787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3010789	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3123307	0.82[EUR][1000 genomes]
rs3124668	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738805	0.84[JPT][hapmap]
rs4543872	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4951475	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4951476	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4951479	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4951662	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs6540778	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6657234	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6666814	0.80[AFR][1000 genomes]
rs6671872	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs6691488	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6692144	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs6699158	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008594	chr1:213110654-213236750	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3002285	RPS6KC1	cis	Artery Tibial	GTEx
rs3002285	ANGEL2	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213154600-213187400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:213154800-213188000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:213154800-213188400	Weak transcription	Spleen	Spleen
4	chr1:213155600-213188000	Weak transcription	Aorta	Aorta
5	chr1:213155600-213188000	Weak transcription	Esophagus	oesophagus
6	chr1:213156200-213187400	Weak transcription	Fetal Brain Male	brain
7	chr1:213156200-213188000	Weak transcription	Pancreas	Pancrea
8	chr1:213158400-213188000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:213160200-213188000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:213160400-213187200	Weak transcription	NHLF	lung
11	chr1:213162000-213184600	Weak transcription	Psoas Muscle	Psoas
12	chr1:213162200-213188000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:213162800-213183000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr1:213163200-213187400	Weak transcription	Stomach Mucosa	stomach
15	chr1:213166000-213182200	Strong transcription	Fetal Intestine Large	intestine
16	chr1:213166000-213184200	Weak transcription	HepG2	liver
17	chr1:213167600-213182600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:213167800-213187000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:213167800-213187000	Weak transcription	Fetal Heart	heart
20	chr1:213167800-213187800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:213168600-213183000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:213169000-213182600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:213169000-213186800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:213169000-213187200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:213169000-213187800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:213169800-213186400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:213170000-213188000	Weak transcription	Colonic Mucosa	Colon
28	chr1:213170600-213187800	Weak transcription	Fetal Kidney	kidney
29	chr1:213172600-213182800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:213172800-213182600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:213173000-213182400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:213173000-213183000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:213173000-213183400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:213173000-213186800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr1:213173000-213187000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:213173200-213183000	Strong transcription	Dnd41	blood
37	chr1:213173400-213182200	Strong transcription	Primary B cells from cord blood	blood
38	chr1:213173600-213182200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr1:213174800-213182600	Strong transcription	Adipose Nuclei	Adipose
40	chr1:213175000-213182800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:213175200-213182600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr1:213175600-213182400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:213176400-213182600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr1:213176800-213182400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:213176800-213182800	Strong transcription	A549	lung
46	chr1:213177200-213187200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:213177400-213182400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:213177400-213182600	Strong transcription	Left Ventricle	heart
49	chr1:213177400-213187800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:213177400-213188000	Weak transcription	Lung	lung

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