Variant report

Variant	rs4540733
Chromosome Location	chr1:212563919-212563920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11119920	0.81[CEU][hapmap]
rs11803766	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12239580	0.81[AFR][1000 genomes]
rs12736502	0.81[CEU][hapmap]
rs12739715	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12755383	0.94[EUR][1000 genomes]
rs17018997	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2166155	0.82[AFR][1000 genomes]
rs2884466	0.80[EUR][1000 genomes]
rs34515259	0.83[EUR][1000 genomes]
rs35556190	0.81[EUR][1000 genomes]
rs35702733	0.93[EUR][1000 genomes]
rs35822123	0.88[EUR][1000 genomes]
rs4336916	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4548507	0.89[AFR][1000 genomes]
rs6666415	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6669027	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6676208	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6693849	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6697910	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6704234	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71646158	0.88[EUR][1000 genomes]
rs71646159	1.00[EUR][1000 genomes]
rs71646161	0.94[EUR][1000 genomes]
rs7533689	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7551910	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4540733	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx
rs4540733	RP11-15I11.3	cis	lung	GTEx
rs4540733	RP11-15I11.3	cis	Thyroid	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr1:212526800-212582800	Weak transcription	Fetal Brain Male	brain
3	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
4	chr1:212534000-212570200	Weak transcription	HSMM	muscle
5	chr1:212534400-212570600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:212538000-212571000	Weak transcription	NH-A	brain
7	chr1:212540400-212575400	Weak transcription	HUVEC	blood vessel
8	chr1:212540600-212564000	Weak transcription	Stomach Mucosa	stomach
9	chr1:212543600-212565200	Weak transcription	Fetal Lung	lung
10	chr1:212553200-212569400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:212553200-212578400	Weak transcription	K562	blood
12	chr1:212556800-212587600	Weak transcription	Small Intestine	intestine
13	chr1:212558600-212578800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:212558600-212580000	Weak transcription	Left Ventricle	heart
15	chr1:212559200-212564800	Weak transcription	HMEC	breast
16	chr1:212560200-212578400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:212560400-212570600	Weak transcription	NHLF	lung
18	chr1:212560400-212580200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:212560600-212566000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:212560600-212567000	Weak transcription	Right Ventricle	heart
21	chr1:212560600-212568000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:212560600-212570000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:212560600-212570200	Weak transcription	Brain Substantia Nigra	brain
24	chr1:212560600-212578200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:212560600-212578800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:212560600-212580200	Weak transcription	HSMMtube	muscle
27	chr1:212560600-212582000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:212560600-212582000	Weak transcription	Gastric	stomach
29	chr1:212561000-212575400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:212561000-212578000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:212561000-212579800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:212561000-212579800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:212561000-212580000	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:212561000-212582400	Weak transcription	Aorta	Aorta
35	chr1:212561200-212572000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:212561800-212565200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:212562000-212564600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:212562000-212570200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:212562000-212578400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:212562200-212564800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
41	chr1:212562400-212564000	ZNF genes & repeats	Dnd41	blood
42	chr1:212562400-212564800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
43	chr1:212562400-212564800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:212562400-212564800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:212562400-212570600	Weak transcription	NHEK	skin
46	chr1:212562600-212564400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
47	chr1:212562600-212564800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
48	chr1:212562600-212571200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:212562800-212564000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:212562800-212564600	ZNF genes & repeats	Primary B cells from cord blood	blood

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