Variant report

Variant	rs12090423
Chromosome Location	chr1:185120779-185120780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:185118743..185122593-chr1:185123034..185127983,12	K562	blood:
2	chr1:185013290..185015307-chr1:185120002..185123053,3	MCF-7	breast:
3	chr1:185116622..185122065-chr1:185122168..185128175,9	MCF-7	breast:
4	chr1:185114176..185116855-chr1:185120494..185122664,2	K562	blood:
5	chr1:185118825..185122081-chr1:185134391..185138048,3	K562	blood:

Variant related genes	Relation type
ENSG00000116668	Chromatin interaction
ENSG00000121481	Chromatin interaction
ENSG00000121486	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10911672	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12059402	1.00[AMR][1000 genomes]
rs12062374	1.00[AMR][1000 genomes]
rs12076847	1.00[AMR][1000 genomes]
rs12093884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74134431	1.00[AMR][1000 genomes]
rs74134432	1.00[AMR][1000 genomes]
rs74134441	1.00[AMR][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	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS 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	69 gene(s)	inside rSNPs	diseases
3	nsv548396	chr1:185038104-185151378	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv521613	chr1:185071831-185171869	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv548397	chr1:185104842-185123630	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185056200-185124200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:185059000-185124800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:185082600-185125400	Weak transcription	Spleen	Spleen
4	chr1:185084200-185124400	Weak transcription	Right Ventricle	heart
5	chr1:185085000-185121400	Weak transcription	NHEK	skin
6	chr1:185085400-185125000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:185087000-185125000	Weak transcription	Gastric	stomach
8	chr1:185089400-185124400	Weak transcription	Colonic Mucosa	Colon
9	chr1:185089600-185121400	Weak transcription	Stomach Mucosa	stomach
10	chr1:185091200-185121400	Weak transcription	Fetal Heart	heart
11	chr1:185096600-185121400	Weak transcription	Hela-S3	cervix
12	chr1:185101000-185121000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:185101600-185125200	Weak transcription	Esophagus	oesophagus
14	chr1:185101800-185120800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:185102000-185120800	Strong transcription	Placenta	Placenta
16	chr1:185102400-185121400	Weak transcription	HMEC	breast
17	chr1:185102400-185124400	Weak transcription	Brain Germinal Matrix	brain
18	chr1:185102600-185124400	Weak transcription	Fetal Brain Male	brain
19	chr1:185102600-185124400	Weak transcription	Small Intestine	intestine
20	chr1:185102800-185121200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr1:185102800-185125000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:185103000-185121400	Weak transcription	Aorta	Aorta
23	chr1:185103000-185124400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:185103200-185121000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:185103200-185121000	Weak transcription	HSMMtube	muscle
26	chr1:185103400-185123600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:185103600-185123800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:185103600-185124400	Weak transcription	Brain Substantia Nigra	brain
29	chr1:185104200-185123000	Weak transcription	HepG2	liver
30	chr1:185104600-185125000	Weak transcription	Pancreas	Pancrea
31	chr1:185105600-185125200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:185105600-185125200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:185105600-185125200	Weak transcription	Lung	lung
34	chr1:185106000-185124400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:185106200-185123400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:185106600-185120800	Strong transcription	Primary B cells from cord blood	blood
37	chr1:185108000-185120800	Strong transcription	Primary B cells from peripheral blood	blood
38	chr1:185108400-185120800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:185108400-185120800	Strong transcription	Liver	Liver
40	chr1:185109200-185124400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:185109400-185120800	Strong transcription	Fetal Thymus	thymus
42	chr1:185109800-185121600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:185110200-185120800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr1:185110800-185121000	Weak transcription	Fetal Intestine Small	intestine
45	chr1:185110800-185124400	Weak transcription	Fetal Stomach	stomach
46	chr1:185111400-185123800	Weak transcription	NHLF	lung
47	chr1:185111600-185124400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:185111600-185124400	Weak transcription	Psoas Muscle	Psoas
49	chr1:185112000-185124400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:185112200-185120800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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