Variant report

Variant	rs12090291
Chromosome Location	chr1:151235586-151235587
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151227043..151228858-chr1:151234009..151236435,4	MCF-7	breast:
2	chr1:151234077..151236106-chr1:151238439..151240160,2	MCF-7	breast:
3	chr1:151234999..151238320-chr1:151251915..151256083,5	MCF-7	breast:
4	chr1:151234387..151237177-chr1:151238975..151242676,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232671	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000159352	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11204788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11204789	1.00[AMR][1000 genomes]
rs11204790	1.00[AMR][1000 genomes]
rs11204797	1.00[AMR][1000 genomes]
rs11204799	1.00[AMR][1000 genomes]
rs11204800	1.00[AMR][1000 genomes]
rs11204801	1.00[AMR][1000 genomes]
rs11204802	1.00[AMR][1000 genomes]
rs11204804	1.00[AMR][1000 genomes]
rs12057875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12058806	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12065050	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12068012	0.82[AFR][1000 genomes]
rs12071605	1.00[AMR][1000 genomes]
rs12073695	1.00[AMR][1000 genomes]
rs12077026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12077958	1.00[AMR][1000 genomes]
rs12080668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082248	1.00[AMR][1000 genomes]
rs12086389	1.00[AMR][1000 genomes]
rs12087802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12089598	0.82[AFR][1000 genomes]
rs12090912	0.82[AFR][1000 genomes]
rs12092749	1.00[AMR][1000 genomes]
rs12094954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61751621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9887870	1.00[AMR][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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh 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	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151227600-151236200	Weak transcription	Spleen	Spleen
2	chr1:151228000-151236200	Weak transcription	Gastric	stomach
3	chr1:151228200-151236400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:151228200-151237000	Weak transcription	Fetal Kidney	kidney
5	chr1:151228400-151236200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:151228400-151236200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:151228400-151236400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:151228400-151236400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:151228400-151236400	Weak transcription	Aorta	Aorta
10	chr1:151228400-151236400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:151228400-151236400	Weak transcription	HSMMtube	muscle
12	chr1:151228400-151236400	Weak transcription	NHDF-Ad	bronchial
13	chr1:151228400-151236600	Weak transcription	Pancreas	Pancrea
14	chr1:151228400-151238200	Weak transcription	Small Intestine	intestine
15	chr1:151228400-151238400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:151228400-151244000	Weak transcription	Right Atrium	heart
17	chr1:151228400-151253400	Weak transcription	Fetal Brain Male	brain
18	chr1:151228600-151236000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:151228600-151236400	Weak transcription	Primary B cells from cord blood	blood
20	chr1:151228600-151236400	Weak transcription	Brain Angular Gyrus	brain
21	chr1:151228600-151236400	Weak transcription	Esophagus	oesophagus
22	chr1:151228600-151236400	Weak transcription	K562	blood
23	chr1:151228600-151236400	Weak transcription	NHLF	lung
24	chr1:151228600-151236600	Weak transcription	HUVEC	blood vessel
25	chr1:151228600-151237000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:151228600-151237000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:151228600-151237000	Weak transcription	HepG2	liver
28	chr1:151228600-151237400	Weak transcription	Right Ventricle	heart
29	chr1:151228600-151238000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:151228600-151244400	Weak transcription	Fetal Heart	heart
31	chr1:151230000-151236200	Weak transcription	GM12878-XiMat	blood
32	chr1:151230400-151237400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:151230600-151244400	Strong transcription	Fetal Stomach	stomach
34	chr1:151231200-151243200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:151231800-151238200	Weak transcription	Psoas Muscle	Psoas
36	chr1:151231800-151243400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:151232800-151244400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:151232800-151244400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:151233800-151242800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:151233800-151243200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:151233800-151244400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:151234000-151236600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr1:151234000-151240600	Strong transcription	Dnd41	blood
44	chr1:151234000-151240600	Strong transcription	HMEC	breast
45	chr1:151234000-151240800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr1:151234000-151240800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:151234000-151241800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:151234000-151243200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:151234000-151244400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:151234000-151245000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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