Variant report

Variant	rs61820936
Chromosome Location	chr1:175953439-175953440
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12402588	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12403164	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12407451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12408191	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12408512	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12409154	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12411139	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16849609	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17351760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17351774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17354043	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4265393	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4292913	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4497165	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4498761	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55779970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56346636	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57729493	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58539711	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59540069	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59801736	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60630667	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61820918	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61820933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61820935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61820954	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61820962	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61820963	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61820964	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61820966	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61820969	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61820971	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61820976	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61821000	0.88[EUR][1000 genomes]
rs61821005	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61821006	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61821032	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61821033	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61821035	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61821058	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61822765	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61822766	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61822768	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6701833	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74127146	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74127162	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7553673	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175904200-175956200	Weak transcription	Psoas Muscle	Psoas
2	chr1:175906400-175962600	Weak transcription	NH-A	brain
3	chr1:175908000-175959400	Weak transcription	NHEK	skin
4	chr1:175940400-175953800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:175946000-175996000	Weak transcription	HMEC	breast
6	chr1:175948200-175957400	Weak transcription	Brain Substantia Nigra	brain
7	chr1:175948200-175961400	Weak transcription	NHLF	lung
8	chr1:175949200-175958600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:175949200-175958600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr1:175949400-175957000	Weak transcription	Osteobl	bone
11	chr1:175949600-175954800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:175949800-175954800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:175950000-175954000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:175950000-175954200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:175950000-175961200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:175950200-175955400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:175950200-175956400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:175950400-175954800	ZNF genes & repeats	Primary B cells from cord blood	blood
19	chr1:175950400-175955000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
20	chr1:175950400-175955000	ZNF genes & repeats	GM12878-XiMat	blood
21	chr1:175950600-175953600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr1:175950600-175954800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
23	chr1:175950800-175953800	ZNF genes & repeats	Liver	Liver
24	chr1:175951000-175953800	ZNF genes & repeats	Adipose Nuclei	Adipose
25	chr1:175951000-175954000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
26	chr1:175951000-175955000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:175951200-175953800	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr1:175951200-175957600	Strong transcription	HSMM	muscle
29	chr1:175951400-175954000	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr1:175951400-175954200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
31	chr1:175951400-175954800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr1:175951600-175953600	Strong transcription	Dnd41	blood
33	chr1:175951600-175954600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr1:175951600-175956200	Strong transcription	Hela-S3	cervix
35	chr1:175951600-175958600	Weak transcription	Fetal Heart	heart
36	chr1:175951800-175953600	ZNF genes & repeats	Fetal Muscle Leg	muscle
37	chr1:175951800-175953800	ZNF genes & repeats	Brain Germinal Matrix	brain
38	chr1:175951800-175954000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
39	chr1:175951800-175954200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
40	chr1:175951800-175954600	ZNF genes & repeats	A549	lung
41	chr1:175951800-175954800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:175951800-175954800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:175951800-175954800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
44	chr1:175951800-175955000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
45	chr1:175951800-175956000	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:175952000-175953600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
47	chr1:175952000-175953800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
48	chr1:175952000-175954000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
49	chr1:175952000-175954200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr1:175952000-175955000	Strong transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links