Variant report

Variant	rs61000820
Chromosome Location	chr1:224565885-224565886
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	chr1:224550099..224552705-chr1:224565403..224568845,3	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10495218	0.83[AFR][1000 genomes]
rs10495221	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11801211	1.00[EUR][1000 genomes]
rs11802182	1.00[EUR][1000 genomes]
rs11807149	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11809688	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11809710	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11810160	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11811935	1.00[EUR][1000 genomes]
rs11812007	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12239466	1.00[EUR][1000 genomes]
rs1499284	1.00[EUR][1000 genomes]
rs16846190	1.00[EUR][1000 genomes]
rs16846212	1.00[EUR][1000 genomes]
rs16846293	1.00[EUR][1000 genomes]
rs16846494	1.00[EUR][1000 genomes]
rs16847675	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847784	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847858	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847870	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847871	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16849419	1.00[EUR][1000 genomes]
rs16849547	1.00[EUR][1000 genomes]
rs1857042	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2068945	1.00[EUR][1000 genomes]
rs2794805	1.00[EUR][1000 genomes]
rs4653586	1.00[EUR][1000 genomes]
rs55712053	1.00[EUR][1000 genomes]
rs57102803	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57469223	1.00[EUR][1000 genomes]
rs57719044	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57967341	1.00[EUR][1000 genomes]
rs58304668	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58649883	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58788859	1.00[EUR][1000 genomes]
rs58814229	1.00[EUR][1000 genomes]
rs59034185	1.00[EUR][1000 genomes]
rs59561838	1.00[EUR][1000 genomes]
rs59577766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59710928	1.00[EUR][1000 genomes]
rs59734390	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs60063902	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs60349703	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60627429	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60715845	1.00[EUR][1000 genomes]
rs60831135	1.00[EUR][1000 genomes]
rs61155217	1.00[EUR][1000 genomes]
rs61278437	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61590597	0.85[AFR][1000 genomes]
rs6426167	1.00[EUR][1000 genomes]
rs6658918	1.00[EUR][1000 genomes]
rs6659109	1.00[EUR][1000 genomes]
rs6674133	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6681611	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6687424	1.00[EUR][1000 genomes]
rs6691181	1.00[EUR][1000 genomes]
rs6702649	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73121865	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123788	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123791	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73125526	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73125529	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73125533	0.81[AFR][1000 genomes]
rs73126411	1.00[EUR][1000 genomes]
rs73128442	1.00[EUR][1000 genomes]
rs73133345	1.00[EUR][1000 genomes]
rs74146372	1.00[EUR][1000 genomes]
rs74146374	1.00[EUR][1000 genomes]
rs74146377	1.00[EUR][1000 genomes]
rs74146381	1.00[EUR][1000 genomes]
rs74146382	1.00[EUR][1000 genomes]
rs74146383	1.00[EUR][1000 genomes]
rs74146384	1.00[EUR][1000 genomes]
rs74146386	1.00[EUR][1000 genomes]
rs74146389	1.00[EUR][1000 genomes]
rs7512165	1.00[EUR][1000 genomes]
rs9661679	1.00[EUR][1000 genomes]
rs9661938	1.00[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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2508330	chr1:224565641-224567115	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224545800-224605000	Weak transcription	Aorta	Aorta
2	chr1:224547000-224593200	Weak transcription	Stomach Mucosa	stomach
3	chr1:224547400-224618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:224547800-224568600	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:224548000-224576000	Weak transcription	Fetal Brain Male	brain
6	chr1:224550400-224568000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:224551000-224568000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:224551400-224568600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:224551600-224566600	Strong transcription	Dnd41	blood
10	chr1:224551600-224568000	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:224551600-224568400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:224553200-224567400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:224553400-224567000	Strong transcription	Adipose Nuclei	Adipose
14	chr1:224553400-224567400	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr1:224553600-224566000	Strong transcription	Fetal Intestine Large	intestine
16	chr1:224553600-224566400	Strong transcription	Fetal Intestine Small	intestine
17	chr1:224553800-224568800	Strong transcription	Fetal Stomach	stomach
18	chr1:224554400-224568200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr1:224554600-224567200	Strong transcription	Liver	Liver
20	chr1:224554600-224567400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:224554800-224568600	Strong transcription	Fetal Brain Female	brain
22	chr1:224555000-224568000	Strong transcription	Brain Anterior Caudate	brain
23	chr1:224555000-224568200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr1:224555200-224566000	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr1:224555200-224568000	Strong transcription	Brain Germinal Matrix	brain
26	chr1:224555800-224581400	Weak transcription	Fetal Heart	heart
27	chr1:224556000-224591000	Weak transcription	Small Intestine	intestine
28	chr1:224558200-224567200	Strong transcription	A549	lung
29	chr1:224560600-224567800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:224561000-224566000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
31	chr1:224561000-224567000	Strong transcription	Lung	lung
32	chr1:224561600-224567000	Strong transcription	Thymus	Thymus
33	chr1:224561800-224567400	Strong transcription	Fetal Kidney	kidney
34	chr1:224562000-224567000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr1:224562400-224566200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:224562600-224567400	Strong transcription	Fetal Lung	lung
37	chr1:224562800-224566200	Genic enhancers	Fetal Thymus	thymus
38	chr1:224562800-224569600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:224563000-224577200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:224563000-224593400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:224563200-224567400	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:224563200-224568600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:224563400-224567400	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr1:224563600-224566200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:224563600-224568000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:224563600-224568200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:224563600-224568600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:224563600-224571200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:224563800-224566000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:224563800-224567000	Strong transcription	Gastric	stomach

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