Variant report

Variant	rs59540069
Chromosome Location	chr1:176070879-176070880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12402588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12403164	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12407451	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12408191	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12408512	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12409154	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12411139	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16849609	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17351760	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17351774	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17354043	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4265393	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4292913	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4497165	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4498761	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55779970	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55815340	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56346636	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57729493	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58539711	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59801736	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60630667	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61820918	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61820933	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61820935	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61820936	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61820954	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61820962	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61820963	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61820964	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61820966	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61820969	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61820971	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61820976	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61821000	0.80[AMR][1000 genomes]
rs61821005	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61821006	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61821032	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61821033	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61821035	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61821055	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61821058	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61821059	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61822660	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61822661	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61822663	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61822765	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61822766	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61822768	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6701833	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs74127146	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs74127162	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7553673	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv872564	chr1:176027978-176102808	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv548246	chr1:176043797-176136273	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv872565	chr1:176058782-176172795	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176028200-176079200	Weak transcription	HSMMtube	muscle
2	chr1:176046600-176082200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:176048800-176107000	Weak transcription	HepG2	liver
4	chr1:176054400-176131600	Weak transcription	NH-A	brain
5	chr1:176055000-176141600	Weak transcription	Hela-S3	cervix
6	chr1:176061200-176072800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:176062400-176072000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
8	chr1:176064400-176072800	ZNF genes & repeats	Primary T cells from cord blood	blood
9	chr1:176064400-176072800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:176064600-176072800	ZNF genes & repeats	Liver	Liver
11	chr1:176065000-176071800	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr1:176065400-176071000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
13	chr1:176065600-176154800	Weak transcription	Aorta	Aorta
14	chr1:176066000-176071400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
15	chr1:176066000-176081800	Weak transcription	GM12878-XiMat	blood
16	chr1:176066800-176071400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
17	chr1:176066800-176071600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:176067200-176071000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
19	chr1:176067200-176071600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
20	chr1:176067800-176071600	ZNF genes & repeats	Primary B cells from cord blood	blood
21	chr1:176068000-176071800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:176068000-176072000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:176068000-176075000	Weak transcription	HSMM	muscle
24	chr1:176068200-176072000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
25	chr1:176068400-176072800	Strong transcription	Dnd41	blood
26	chr1:176068400-176079200	Weak transcription	Fetal Heart	heart
27	chr1:176068600-176071400	ZNF genes & repeats	Fetal Brain Female	brain
28	chr1:176068600-176071400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
29	chr1:176068600-176071400	ZNF genes & repeats	Ovary	ovary
30	chr1:176068600-176072000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
31	chr1:176068600-176072400	ZNF genes & repeats	Fetal Muscle Leg	muscle
32	chr1:176068600-176077000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:176068600-176087600	Weak transcription	NHLF	lung
34	chr1:176068800-176071400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:176068800-176071400	Strong transcription	Fetal Stomach	stomach
36	chr1:176068800-176072600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:176068800-176072800	ZNF genes & repeats	Fetal Intestine Small	intestine
38	chr1:176069000-176071000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:176069000-176071000	Strong transcription	Fetal Lung	lung
40	chr1:176069000-176072400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:176069000-176080800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:176069000-176090200	Weak transcription	Fetal Kidney	kidney
43	chr1:176069000-176116400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:176069000-176139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:176069200-176071000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:176069200-176071200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr1:176069200-176071200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:176069200-176071800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:176069200-176072200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:176069200-176072200	Weak transcription	NHDF-Ad	bronchial

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