Variant report

Variant	rs3010016
Chromosome Location	chr1:212227089-212227090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212223004..212226012-chr1:212226300..212230375,4	K562	blood:
2	chr1:212225791..212228790-chr1:212457978..212459745,2	K562	blood:
3	chr1:212219058..212220568-chr1:212226723..212229507,2	K562	blood:
4	chr1:212225925..212230498-chr1:212230640..212238482,9	K562	blood:

Variant related genes	Relation type
ENSG00000220749	Chromatin interaction
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1586660	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2358439	0.85[AFR][1000 genomes]
rs2808386	1.00[AMR][1000 genomes]
rs2808388	1.00[AMR][1000 genomes]
rs2808389	1.00[AMR][1000 genomes]
rs2970604	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2993535	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2993538	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2993539	0.87[AMR][1000 genomes]
rs2993545	0.83[EUR][1000 genomes]
rs3009991	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3009997	0.83[EUR][1000 genomes]
rs3010029	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4951436	1.00[EUR][1000 genomes]
rs6675701	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6690508	0.96[EUR][1000 genomes]
rs7520161	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7535988	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7545292	0.86[AFR][1000 genomes];0.96[EUR][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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3010016	LPGAT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212209600-212253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:212210400-212227400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:212210400-212228800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:212210400-212228800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:212210400-212228800	Weak transcription	Fetal Intestine Large	intestine
6	chr1:212210600-212227400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:212210600-212229200	Weak transcription	Fetal Brain Female	brain
8	chr1:212210800-212241200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:212211000-212227200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:212211400-212229200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:212211600-212227400	Weak transcription	Fetal Lung	lung
12	chr1:212212000-212228400	Weak transcription	Brain Germinal Matrix	brain
13	chr1:212212000-212229200	Weak transcription	Fetal Kidney	kidney
14	chr1:212214400-212227200	Weak transcription	NHEK	skin
15	chr1:212214400-212228000	Weak transcription	NH-A	brain
16	chr1:212214400-212228200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:212214400-212278000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:212214600-212227400	Weak transcription	Thymus	Thymus
19	chr1:212214600-212228400	Weak transcription	NHLF	lung
20	chr1:212214600-212228800	Strong transcription	Hela-S3	cervix
21	chr1:212215600-212229200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:212215600-212233000	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:212215800-212228800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:212215800-212229000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:212216000-212229200	Strong transcription	Fetal Thymus	thymus
26	chr1:212216200-212233200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:212216400-212229400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:212216600-212227600	Weak transcription	Osteobl	bone
29	chr1:212216800-212229000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr1:212217000-212232800	Strong transcription	Dnd41	blood
31	chr1:212217400-212228600	Weak transcription	Fetal Intestine Small	intestine
32	chr1:212218000-212231000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:212218000-212231800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:212218600-212228600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr1:212219400-212228800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:212219800-212228400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:212220000-212228400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:212220600-212229200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:212220800-212227200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr1:212221200-212227600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:212222600-212228200	Strong transcription	GM12878-XiMat	blood
42	chr1:212222800-212228400	Strong transcription	A549	lung
43	chr1:212223000-212228400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:212223000-212228600	Weak transcription	HUVEC	blood vessel
45	chr1:212223200-212228600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:212223400-212228600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:212223600-212227400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:212224600-212228800	Weak transcription	HSMM	muscle
49	chr1:212225000-212227200	Weak transcription	HepG2	liver
50	chr1:212225400-212229000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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