Variant report

Variant	rs12060644
Chromosome Location	chr1:47084531-47084532
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47068429..47072503-chr1:47081068..47085092,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079277	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11211329	0.90[AFR][1000 genomes]
rs1258010	1.00[EUR][1000 genomes]
rs1258022	1.00[EUR][1000 genomes]
rs1767598	1.00[EUR][1000 genomes]
rs1767612	1.00[EUR][1000 genomes]
rs2274422	1.00[EUR][1000 genomes]
rs3737742	1.00[EUR][1000 genomes]
rs57340268	1.00[EUR][1000 genomes]
rs57954022	1.00[EUR][1000 genomes]
rs58591480	1.00[EUR][1000 genomes]
rs60081306	1.00[EUR][1000 genomes]
rs7549865	1.00[EUR][1000 genomes]
rs946321	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv522319	chr1:47080741-47094267	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47082800-47089600	Weak transcription	Small Intestine	intestine
2	chr1:47083000-47085600	Enhancers	GM12878-XiMat	blood
3	chr1:47083000-47085800	Enhancers	Primary B cells from peripheral blood	blood
4	chr1:47083000-47088000	Weak transcription	Spleen	Spleen
5	chr1:47083000-47090800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:47083000-47094400	Weak transcription	Primary T cells from cord blood	blood
7	chr1:47083000-47094600	Weak transcription	Right Ventricle	heart
8	chr1:47083000-47097200	Weak transcription	Gastric	stomach
9	chr1:47083000-47100000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:47083200-47084800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:47083200-47087000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:47083200-47087000	Weak transcription	HSMM	muscle
13	chr1:47083200-47087400	Weak transcription	Fetal Intestine Large	intestine
14	chr1:47083200-47087400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:47083200-47087600	Weak transcription	NHEK	skin
16	chr1:47083200-47088000	Weak transcription	Placenta	Placenta
17	chr1:47083200-47088000	Weak transcription	NH-A	brain
18	chr1:47083200-47094400	Weak transcription	Brain Angular Gyrus	brain
19	chr1:47083200-47094600	Weak transcription	Liver	Liver
20	chr1:47083200-47095400	Weak transcription	Fetal Thymus	thymus
21	chr1:47083200-47095600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:47083200-47097200	Weak transcription	Primary B cells from cord blood	blood
23	chr1:47083200-47097200	Weak transcription	Aorta	Aorta
24	chr1:47083200-47097200	Weak transcription	Thymus	Thymus
25	chr1:47083200-47100200	Weak transcription	Psoas Muscle	Psoas
26	chr1:47083200-47104600	Weak transcription	Stomach Mucosa	stomach
27	chr1:47083200-47115000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:47083400-47086600	Weak transcription	Hela-S3	cervix
29	chr1:47083400-47086600	Enhancers	K562	blood
30	chr1:47083400-47087400	Weak transcription	Colonic Mucosa	Colon
31	chr1:47083400-47087400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:47083400-47087600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:47083400-47087600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:47083400-47087800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:47083400-47087800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:47083400-47089200	Weak transcription	Right Atrium	heart
37	chr1:47083400-47092200	Weak transcription	Pancreas	Pancrea
38	chr1:47083400-47094200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:47083400-47094200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:47083400-47094600	Weak transcription	Adipose Nuclei	Adipose
41	chr1:47083400-47094800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:47083400-47095000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:47083400-47095600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:47083400-47095600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:47083400-47095600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:47083400-47095600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:47083400-47096800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:47083400-47097000	Weak transcription	Colon Smooth Muscle	Colon
49	chr1:47083400-47097400	Weak transcription	Brain Substantia Nigra	brain
50	chr1:47083400-47113200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links