Variant report

Variant	rs1890345
Chromosome Location	chr1:212102905-212102906
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:211907600..211909602-chr1:212100181..212103074,3	MCF-7	breast:
2	chr1:212089622..212092139-chr1:212102871..212105783,2	K562	blood:
3	chr1:151965041..151965732-chr1:212102304..212102975,2	Hela-S3	cervix:
4	chr1:212081479..212083275-chr1:212101212..212103097,2	K562	blood:
5	chr1:212100825..212103790-chr1:212103837..212105355,2	K562	blood:
6	chr1:212101718..212103462-chr1:212208564..212211314,2	K562	blood:
7	chr1:212101758..212105730-chr1:212107353..212109879,3	MCF-7	breast:
8	chr1:212002995..212005657-chr1:212102494..212104285,2	K562	blood:
9	chr1:212002998..212004643-chr1:212102667..212104537,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000229258	Chromatin interaction
ENSG00000143493	Chromatin interaction
ENSG00000233626	Chromatin interaction
ENSG00000123684	Chromatin interaction
ENSG00000143476	Chromatin interaction
ENSG00000197747	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10494949	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1052351	1.00[EUR][1000 genomes]
rs17017993	1.00[CEU][hapmap]
rs17018170	0.81[EUR][1000 genomes]
rs17018182	0.81[EUR][1000 genomes]
rs17018199	0.81[EUR][1000 genomes]
rs17018234	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17018237	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17018244	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17018248	1.00[EUR][1000 genomes]
rs17018249	1.00[EUR][1000 genomes]
rs17018262	1.00[EUR][1000 genomes]
rs17018284	1.00[EUR][1000 genomes]
rs17018310	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17018311	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17018329	1.00[EUR][1000 genomes]
rs17018332	1.00[EUR][1000 genomes]
rs17018335	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17018340	1.00[EUR][1000 genomes]
rs17018342	1.00[EUR][1000 genomes]
rs17018375	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17018392	1.00[EUR][1000 genomes]
rs17018399	1.00[EUR][1000 genomes]
rs17018403	0.87[EUR][1000 genomes]
rs17018418	0.87[EUR][1000 genomes]
rs17018426	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs17018435	0.87[EUR][1000 genomes]
rs17018511	1.00[CEU][hapmap]
rs1933594	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs2358385	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs41275374	1.00[EUR][1000 genomes]
rs41502452	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs5780667	1.00[EUR][1000 genomes]
rs73091032	0.81[EUR][1000 genomes]
rs73091037	0.81[EUR][1000 genomes]
rs7415591	0.87[EUR][1000 genomes]
rs9659156	1.00[YRI][hapmap]
rs9662399	1.00[YRI][hapmap]
rs9662621	1.00[YRI][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1890345	LPGAT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212084800-212113000	Weak transcription	Brain Anterior Caudate	brain
2	chr1:212094200-212103200	Weak transcription	Small Intestine	intestine
3	chr1:212098800-212106000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:212100600-212104400	Enhancers	Fetal Intestine Small	intestine
5	chr1:212100600-212104800	Enhancers	Fetal Intestine Large	intestine
6	chr1:212100600-212109000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:212100800-212103400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:212100800-212103400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:212101000-212103600	Enhancers	HMEC	breast
10	chr1:212101200-212103400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:212101400-212103000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:212101400-212103000	Flanking Active TSS	K562	blood
13	chr1:212101400-212103200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr1:212101400-212103200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr1:212101400-212103600	Enhancers	Placenta	Placenta
16	chr1:212101400-212107800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:212101600-212103200	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:212101600-212103200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:212101600-212103400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:212101600-212103400	Enhancers	Liver	Liver
21	chr1:212101600-212103400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr1:212101600-212103600	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr1:212101800-212103000	Enhancers	H9 Cell Line	embryonic stem cell
24	chr1:212101800-212103000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:212101800-212103000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr1:212101800-212103000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr1:212101800-212103000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:212101800-212103000	Enhancers	Gastric	stomach
29	chr1:212101800-212103200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:212101800-212103400	Flanking Active TSS	Hela-S3	cervix
31	chr1:212101800-212103600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr1:212101800-212103600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:212102000-212103000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr1:212102000-212103000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:212102000-212103000	Flanking Active TSS	A549	lung
36	chr1:212102000-212103600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:212102000-212103600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:212102000-212106200	Weak transcription	Right Atrium	heart
39	chr1:212102000-212109000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:212102200-212103000	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr1:212102200-212103000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr1:212102200-212103200	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr1:212102200-212103400	Enhancers	Fetal Lung	lung
44	chr1:212102200-212103400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr1:212102200-212103400	Flanking Active TSS	HepG2	liver
46	chr1:212102200-212103600	Enhancers	Esophagus	oesophagus
47	chr1:212102200-212103600	Enhancers	NHEK	skin
48	chr1:212102200-212104200	Enhancers	Lung	lung
49	chr1:212102400-212103000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:212102400-212103200	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links