Variant report

Variant	rs17018540
Chromosome Location	chr1:212284779-212284780
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212278390..212281582-chr1:212282096..212285303,4	K562	blood:
2	chr1:212280082..212281829-chr1:212283575..212285345,3	K562	blood:
3	chr1:212283228..212285766-chr1:212457122..212460102,2	K562	blood:
4	chr1:212283620..212286277-chr1:212286773..212289350,3	K562	blood:

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10494949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1052351	1.00[AMR][1000 genomes]
rs17018234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17018237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17018244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17018248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17018249	1.00[AMR][1000 genomes]
rs17018262	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17018284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17018310	1.00[AFR][1000 genomes]
rs17018311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17018329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17018332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17018340	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17018342	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17018375	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17018392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17018399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17018403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17018418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17018426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17018435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17018458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17018472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17018511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17018514	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17018516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1933594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41275374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41502452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7415591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[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
rs17018540	LPGAT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212262200-212289200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:212267200-212287000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:212271600-212287000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:212272000-212285400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:212272000-212285800	Weak transcription	Lung	lung
6	chr1:212272000-212291000	Weak transcription	Left Ventricle	heart
7	chr1:212274200-212287000	Weak transcription	HMEC	breast
8	chr1:212274200-212301600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:212274400-212308200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:212275400-212286600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:212277000-212298200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:212277800-212285000	Enhancers	Fetal Lung	lung
13	chr1:212279000-212291800	Weak transcription	HepG2	liver
14	chr1:212279200-212285600	Strong transcription	Hela-S3	cervix
15	chr1:212279800-212286600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:212279800-212287400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:212280000-212299600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:212280400-212285400	Enhancers	Thymus	Thymus
19	chr1:212281200-212285200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:212281200-212285400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:212281200-212285800	Enhancers	Primary T cells from cord blood	blood
22	chr1:212281200-212308400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:212281400-212285000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:212281400-212287200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:212281600-212288600	Strong transcription	Dnd41	blood
26	chr1:212281800-212284800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:212281800-212285600	Enhancers	Fetal Heart	heart
28	chr1:212282000-212285400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:212282000-212285400	Genic enhancers	K562	blood
30	chr1:212282400-212285000	Enhancers	Fetal Stomach	stomach
31	chr1:212282600-212285800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:212282600-212292000	Weak transcription	GM12878-XiMat	blood
33	chr1:212282800-212287200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:212282800-212292000	Weak transcription	Right Atrium	heart
35	chr1:212283000-212286600	Weak transcription	Fetal Intestine Small	intestine
36	chr1:212283000-212289400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:212283200-212285400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:212283200-212287400	Strong transcription	A549	lung
39	chr1:212283400-212285200	Enhancers	Fetal Brain Male	brain
40	chr1:212283400-212287000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:212283600-212284800	Enhancers	Fetal Muscle Leg	muscle
42	chr1:212283800-212285200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:212283800-212300400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:212284000-212298400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:212284200-212285600	Enhancers	Psoas Muscle	Psoas
46	chr1:212284400-212284800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:212284400-212285600	Genic enhancers	Fetal Thymus	thymus
48	chr1:212284400-212291600	Weak transcription	Stomach Mucosa	stomach
49	chr1:212284400-212292400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:212284400-212294600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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