Variant report

Variant	rs12566373
Chromosome Location	chr1:94022571-94022572
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	chr1:94021033..94023229-chr1:94024981..94026718,2	MCF-7	breast:
2	chr1:94021702..94024985-chr1:94029081..94032053,4	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12563504	0.83[EUR][1000 genomes]
rs17110076	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2295330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs236266	1.00[CEU][hapmap]
rs236295	1.00[CEU][hapmap]
rs236296	1.00[CEU][hapmap]
rs236321	0.80[CHB][hapmap]
rs236322	0.90[CHB][hapmap]
rs236330	0.90[CHB][hapmap]
rs236331	0.90[CHB][hapmap]
rs236332	0.91[CHB][hapmap]
rs236335	0.90[CHB][hapmap]
rs35115771	0.83[EUR][1000 genomes]
rs3754189	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3767973	0.82[EUR][1000 genomes]
rs3767975	0.90[CHB][hapmap]
rs3767976	0.80[CHB][hapmap]
rs3767977	0.90[CHB][hapmap]
rs3767979	1.00[CEU][hapmap]
rs3767991	1.00[CEU][hapmap]
rs57012808	0.82[EUR][1000 genomes]
rs57466479	0.82[EUR][1000 genomes]
rs57914444	0.82[EUR][1000 genomes]
rs59777284	0.82[EUR][1000 genomes]
rs6541380	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6661488	0.90[CHB][hapmap]
rs6674143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6699020	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7524368	0.82[EUR][1000 genomes]
rs7546785	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011853	chr1:93966450-94039005	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93973400-94032000	Weak transcription	Esophagus	oesophagus
2	chr1:93995000-94045000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:94012800-94024800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr1:94014000-94025200	Weak transcription	Aorta	Aorta
5	chr1:94014600-94025000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:94016000-94025200	Weak transcription	Ovary	ovary
7	chr1:94016800-94031600	Weak transcription	Fetal Stomach	stomach
8	chr1:94018000-94023800	Weak transcription	Primary B cells from cord blood	blood
9	chr1:94018400-94024600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:94018400-94031600	Weak transcription	Spleen	Spleen
11	chr1:94018600-94024600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:94018600-94024800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:94018600-94031600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:94018600-94037400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:94019000-94023400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:94019000-94024000	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:94019000-94025000	Weak transcription	Placenta	Placenta
18	chr1:94019000-94025000	Weak transcription	NHEK	skin
19	chr1:94019000-94025200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:94019000-94025200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:94019000-94025200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:94019000-94026000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:94019000-94031800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:94019000-94032000	Weak transcription	Brain Germinal Matrix	brain
25	chr1:94019200-94025000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:94019200-94025000	Weak transcription	Fetal Brain Female	brain
27	chr1:94019200-94025200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:94019200-94025200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:94019200-94031200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:94019200-94037400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:94019400-94024000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:94020200-94034200	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:94020400-94025200	Weak transcription	Liver	Liver
34	chr1:94020400-94025200	Weak transcription	Fetal Kidney	kidney
35	chr1:94020600-94024200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:94020600-94025000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:94020600-94025000	Weak transcription	NHDF-Ad	bronchial
38	chr1:94020600-94025200	Weak transcription	Adipose Nuclei	Adipose
39	chr1:94020600-94025200	Weak transcription	NHLF	lung
40	chr1:94020800-94023000	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr1:94020800-94023600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:94020800-94024000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:94020800-94024600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:94020800-94024600	Weak transcription	Osteobl	bone
45	chr1:94020800-94024800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:94020800-94025000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:94020800-94025000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:94020800-94025200	Weak transcription	Left Ventricle	heart
49	chr1:94020800-94025200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr1:94020800-94025400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links