Variant report

Variant	rs60063902
Chromosome Location	chr1:224565769-224565770
allele	A/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: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10495218	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10495221	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11800357	0.86[AMR][1000 genomes]
rs11804538	0.86[AMR][1000 genomes]
rs11807149	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11809688	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11809710	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11810160	1.00[AMR][1000 genomes]
rs11812007	1.00[AMR][1000 genomes]
rs16847675	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16847784	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16847858	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16847870	0.93[AMR][1000 genomes]
rs16847871	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1857042	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2211327	0.86[AMR][1000 genomes]
rs57102803	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs57719044	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs58304668	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58649883	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs59577766	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs59734390	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60349703	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60627429	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs61000820	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs61278437	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs61590597	0.86[AMR][1000 genomes]
rs6674133	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6681611	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6702649	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs73121865	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs73123788	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs73123791	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs73125526	1.00[AMR][1000 genomes]
rs73125529	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs73125533	0.89[AFR][1000 genomes]
rs73125540	0.86[AMR][1000 genomes]
rs73125543	0.86[AFR][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	chr1:224551200-224565800	Strong transcription	Primary B cells from cord blood	blood
9	chr1:224551400-224568600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:224551600-224566600	Strong transcription	Dnd41	blood
11	chr1:224551600-224568000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:224551600-224568400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:224552800-224565800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:224553200-224567400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:224553400-224567000	Strong transcription	Adipose Nuclei	Adipose
16	chr1:224553400-224567400	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr1:224553600-224566000	Strong transcription	Fetal Intestine Large	intestine
18	chr1:224553600-224566400	Strong transcription	Fetal Intestine Small	intestine
19	chr1:224553800-224568800	Strong transcription	Fetal Stomach	stomach
20	chr1:224554400-224568200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:224554600-224567200	Strong transcription	Liver	Liver
22	chr1:224554600-224567400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:224554800-224568600	Strong transcription	Fetal Brain Female	brain
24	chr1:224555000-224568000	Strong transcription	Brain Anterior Caudate	brain
25	chr1:224555000-224568200	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr1:224555200-224566000	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr1:224555200-224568000	Strong transcription	Brain Germinal Matrix	brain
28	chr1:224555800-224581400	Weak transcription	Fetal Heart	heart
29	chr1:224556000-224591000	Weak transcription	Small Intestine	intestine
30	chr1:224558200-224567200	Strong transcription	A549	lung
31	chr1:224560600-224567800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr1:224561000-224566000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr1:224561000-224567000	Strong transcription	Lung	lung
34	chr1:224561600-224567000	Strong transcription	Thymus	Thymus
35	chr1:224561800-224567400	Strong transcription	Fetal Kidney	kidney
36	chr1:224562000-224567000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr1:224562400-224566200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:224562600-224567400	Strong transcription	Fetal Lung	lung
39	chr1:224562800-224565800	Genic enhancers	HSMM	muscle
40	chr1:224562800-224566200	Genic enhancers	Fetal Thymus	thymus
41	chr1:224562800-224569600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:224563000-224577200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:224563000-224593400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:224563200-224567400	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:224563200-224568600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:224563400-224567400	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr1:224563600-224566200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:224563600-224568000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:224563600-224568200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:224563600-224568600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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