Variant report

Variant	rs60952228
Chromosome Location	chr1:46160253-46160254
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46158939..46160922-chr1:46213584..46216155,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs34965970	1.00[AMR][1000 genomes]
rs35210931	1.00[AMR][1000 genomes]
rs4297232	1.00[AMR][1000 genomes]
rs56695029	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57402001	1.00[AMR][1000 genomes]
rs57813129	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59974520	1.00[AMR][1000 genomes]
rs60301454	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60660559	0.84[AFR][1000 genomes]
rs61169182	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
2	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
5	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv1014128	chr1:46097670-46394540	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
7	nsv1010054	chr1:46144479-46320493	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
8	nsv1006861	chr1:46144479-46417621	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
9	nsv1003049	chr1:46144479-46476149	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
10	nsv870511	chr1:46148138-46245423	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv871233	chr1:46153203-46311275	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
12	nsv945922	chr1:46158774-46160316	Strong transcription Weak transcription	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv1008219	chr1:46160098-46493958	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
14	nsv534943	chr1:46160098-46493958	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46154600-46160600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:46154600-46163000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:46154600-46169400	Weak transcription	Ovary	ovary
4	chr1:46154600-46177200	Weak transcription	Aorta	Aorta
5	chr1:46154600-46180000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:46154600-46188600	Weak transcription	Fetal Heart	heart
7	chr1:46154600-46206600	Weak transcription	Brain Substantia Nigra	brain
8	chr1:46154800-46160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:46154800-46186000	Weak transcription	Psoas Muscle	Psoas
10	chr1:46154800-46192600	Weak transcription	Pancreas	Pancrea
11	chr1:46155000-46161400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:46155000-46185200	Weak transcription	Colonic Mucosa	Colon
13	chr1:46155000-46187000	Weak transcription	NHLF	lung
14	chr1:46155000-46215800	Weak transcription	Small Intestine	intestine
15	chr1:46155200-46177600	Weak transcription	Fetal Brain Male	brain
16	chr1:46155200-46178800	Weak transcription	Stomach Mucosa	stomach
17	chr1:46155400-46161000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:46155400-46163200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:46155400-46163600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:46155600-46160600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:46155600-46161400	Strong transcription	Brain Germinal Matrix	brain
22	chr1:46155600-46162200	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:46155600-46163600	Strong transcription	Placenta	Placenta
24	chr1:46155600-46204600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:46155800-46163600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:46155800-46163600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:46155800-46163600	Strong transcription	Fetal Muscle Leg	muscle
28	chr1:46155800-46188400	Weak transcription	Hela-S3	cervix
29	chr1:46155800-46215600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:46156000-46161200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:46156000-46161200	Strong transcription	GM12878-XiMat	blood
32	chr1:46156000-46162400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:46156000-46163000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr1:46156000-46163000	Strong transcription	Fetal Brain Female	brain
35	chr1:46156000-46163000	Strong transcription	Dnd41	blood
36	chr1:46156000-46163200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr1:46156000-46177200	Weak transcription	Lung	lung
38	chr1:46156200-46163000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr1:46156200-46170600	Weak transcription	HepG2	liver
40	chr1:46156400-46160600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:46156400-46160800	Strong transcription	HUVEC	blood vessel
42	chr1:46156400-46162600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:46156400-46163000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:46156400-46163200	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr1:46156600-46160400	Strong transcription	Primary hematopoietic stem cells	blood
46	chr1:46156600-46161000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr1:46156600-46161600	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr1:46156600-46162000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:46156600-46162400	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr1:46156600-46162600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links