Variant report

Variant	rs1054733
Chromosome Location	chr1:212989840-212989841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212987979..212990902-chr1:213030404..213032283,2	MCF-7	breast:
2	chr1:212965331..212966831-chr1:212989639..212991384,2	K562	blood:

Variant related genes	Relation type
ENSG00000203705	Chromatin interaction
ENSG00000162769	Chromatin interaction
ENSG00000198468	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10494955	0.85[ASN][1000 genomes]
rs10863993	0.83[ASN][1000 genomes]
rs10863998	0.84[ASN][1000 genomes]
rs10863999	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10864000	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10864001	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11120011	0.81[ASN][1000 genomes]
rs11120012	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11120013	0.81[ASN][1000 genomes]
rs11120024	0.85[ASN][1000 genomes]
rs11120025	0.80[ASN][1000 genomes]
rs11120026	0.85[ASN][1000 genomes]
rs11120027	0.85[ASN][1000 genomes]
rs11120032	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11120037	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11120039	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1133462	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12064985	0.87[ASN][1000 genomes]
rs12088916	0.83[ASN][1000 genomes]
rs12095846	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12097897	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12125321	0.81[EUR][1000 genomes]
rs12126017	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12130945	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12132316	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12136046	0.83[ASN][1000 genomes]
rs12136834	0.83[ASN][1000 genomes]
rs12565557	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12722742	0.83[ASN][1000 genomes]
rs12734406	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12734543	0.94[ASN][1000 genomes]
rs12737398	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12741704	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12743402	0.81[ASN][1000 genomes]
rs12744602	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2359322	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3820679	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3862953	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4951463	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4951638	0.81[ASN][1000 genomes]
rs6540761	0.81[EUR][1000 genomes]
rs6540763	0.82[ASN][1000 genomes]
rs6661720	0.83[ASN][1000 genomes]
rs6679350	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6679549	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6689604	0.91[ASN][1000 genomes]
rs6690689	0.83[ASN][1000 genomes]
rs6693311	0.83[ASN][1000 genomes]
rs6697507	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6700410	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6702025	0.81[EUR][1000 genomes]
rs6702611	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7554105	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7556272	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1054733	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs1054733	LQK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212965800-212992600	Weak transcription	Lung	lung
2	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
3	chr1:212966400-212990200	Weak transcription	Right Ventricle	heart
4	chr1:212969600-212993000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:212971200-212990200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:212972400-212993600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:212972600-212990200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:212975800-212997800	Weak transcription	Brain Substantia Nigra	brain
9	chr1:212976000-212990200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:212976000-212990200	Weak transcription	Fetal Brain Female	brain
11	chr1:212976200-212998800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:212979200-212994200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:212979600-212992000	Weak transcription	Brain Anterior Caudate	brain
14	chr1:212979600-212993200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:212979600-213001000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:212980800-213001000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:212981000-212990400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:212981600-212990400	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:212982400-212990400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:212982600-212990000	Weak transcription	Hela-S3	cervix
21	chr1:212982600-212990400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:212982600-212992800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:212982800-212992200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:212982800-212992600	Weak transcription	Placenta	Placenta
25	chr1:212987000-212992200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:212987200-212993000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:212987400-212991200	Enhancers	Fetal Intestine Large	intestine
28	chr1:212988200-212990000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:212988200-212990000	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:212988200-212990400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:212988200-212990600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:212988200-212992000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:212988200-212992600	Weak transcription	Primary B cells from cord blood	blood
34	chr1:212988400-212990000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:212988400-212998800	Weak transcription	Adipose Nuclei	Adipose
36	chr1:212988600-212990000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:212988600-212992400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr1:212988600-212993000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:212988600-212993200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:212988600-212998400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:212988800-212990000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:212988800-212990000	Weak transcription	Stomach Mucosa	stomach
43	chr1:212988800-212990400	Weak transcription	Liver	Liver
44	chr1:212988800-212990400	Weak transcription	Left Ventricle	heart
45	chr1:212988800-212990600	Weak transcription	Primary T cells from cord blood	blood
46	chr1:212988800-212990600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:212988800-212990600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:212988800-212990600	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr1:212988800-212991400	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:212988800-212992600	Weak transcription	GM12878-XiMat	blood

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