Variant report

Variant	rs7545292
Chromosome Location	chr1:212279058-212279059
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212278071..212280364-chr1:212458201..212459843,2	K562	blood:
2	chr1:212259952..212261653-chr1:212277929..212279686,2	K562	blood:
3	chr1:212278390..212281582-chr1:212282096..212285303,4	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]
rs10863938	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs1586660	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2788130	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2788135	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2788137	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2788138	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs2788141	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2808380	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2808388	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2970586	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2970604	1.00[CEU][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes]
rs2993524	0.88[TSI][hapmap]
rs2993535	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs2993536	1.00[TSI][hapmap]
rs2993540	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2993545	0.87[AMR][1000 genomes]
rs2993546	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs3009986	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs3009991	0.87[AMR][1000 genomes]
rs3009994	0.90[GIH][hapmap];0.90[TSI][hapmap]
rs3009997	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3010008	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs3010014	0.88[GIH][hapmap];1.00[TSI][hapmap]
rs3010016	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3010022	0.90[GIH][hapmap];1.00[TSI][hapmap]
rs3010029	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4951436	0.96[EUR][1000 genomes]
rs6675701	1.00[CEU][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6690508	1.00[EUR][1000 genomes]
rs7520161	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7535988	0.88[AFR][1000 genomes];0.98[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
rs7545292	LPGAT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212241600-212284600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:212262000-212283000	Weak transcription	NH-A	brain
3	chr1:212262000-212284400	Weak transcription	Osteobl	bone
4	chr1:212262200-212279600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:212262200-212289200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:212264400-212282400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr1:212267200-212287000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:212268600-212282800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:212269800-212279600	Strong transcription	Dnd41	blood
10	chr1:212270400-212280400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:212270600-212280200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:212270800-212279800	Strong transcription	Fetal Thymus	thymus
13	chr1:212271400-212280000	Strong transcription	GM12878-XiMat	blood
14	chr1:212271600-212280400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:212271600-212287000	Weak transcription	Primary B cells from cord blood	blood
16	chr1:212271800-212280200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:212272000-212281000	Weak transcription	Esophagus	oesophagus
18	chr1:212272000-212285400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:212272000-212285800	Weak transcription	Lung	lung
20	chr1:212272000-212291000	Weak transcription	Left Ventricle	heart
21	chr1:212272200-212279600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:212272200-212280200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:212272200-212280200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:212272200-212282800	Weak transcription	Placenta	Placenta
25	chr1:212272600-212281600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:212274200-212287000	Weak transcription	HMEC	breast
27	chr1:212274200-212301600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:212274400-212279800	Weak transcription	Thymus	Thymus
29	chr1:212274400-212280600	Weak transcription	HUVEC	blood vessel
30	chr1:212274400-212282200	Weak transcription	NHEK	skin
31	chr1:212274400-212284200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:212274400-212308200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:212274600-212282400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:212274600-212283600	Weak transcription	Fetal Muscle Leg	muscle
35	chr1:212274800-212279800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:212275400-212282600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr1:212275400-212286600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:212275600-212280800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:212275600-212280800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:212276600-212282000	Strong transcription	K562	blood
41	chr1:212276800-212280600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:212276800-212283000	Enhancers	Fetal Intestine Small	intestine
43	chr1:212277000-212280200	Enhancers	Fetal Intestine Large	intestine
44	chr1:212277000-212298200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:212277400-212279600	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr1:212277600-212279200	Enhancers	Fetal Stomach	stomach
47	chr1:212277600-212279200	Weak transcription	Hela-S3	cervix
48	chr1:212277600-212279400	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr1:212277600-212280800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr1:212277600-212281200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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