Variant report

Variant	rs12090501
Chromosome Location	chr1:46595329-46595330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:46595155-46595457	H1-neurons	neurons:	n/a	n/a
2	REST	chr1:46594809-46600272	H1-neurons	neurons:	n/a	chr1:46594846-46594866 chr1:46599316-46599334 chr1:46598398-46598411 chr1:46594846-46594866 chr1:46599370-46599390

No.	Distal block	Cell Line	Cell type
1	chr1:46592691..46601867-chr1:46642778..46650670,25	MCF-7	breast:
2	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
3	chr1:45184920..45187380-chr1:46595320..46596942,2	K562	blood:
4	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:
5	chr1:46539301..46542109-chr1:46593779..46595695,2	K562	blood:
6	chr1:46595304..46602065-chr1:46660247..46665309,8	MCF-7	breast:
7	chr1:46531892..46533650-chr1:46593425..46595448,2	MCF-7	breast:
8	chr1:46500927..46503041-chr1:46594569..46596961,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227857	TF binding region
ENSG00000117472	Chromatin interaction
ENSG00000085998	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000250719	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1085240	0.84[ASN][1000 genomes]
rs11211257	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1416706	0.84[ASN][1000 genomes]
rs1473840	0.85[ASN][1000 genomes]
rs1588663	0.85[ASN][1000 genomes]
rs1612419	0.85[ASN][1000 genomes]
rs1613296	0.85[ASN][1000 genomes]
rs1707302	0.86[ASN][1000 genomes]
rs1707303	0.96[ASN][1000 genomes]
rs1707317	0.84[ASN][1000 genomes]
rs1707322	0.84[ASN][1000 genomes]
rs1707337	0.84[ASN][1000 genomes]
rs1707338	0.84[ASN][1000 genomes]
rs1707339	0.82[ASN][1000 genomes]
rs1768800	0.85[ASN][1000 genomes]
rs1768801	0.85[ASN][1000 genomes]
rs1768802	0.85[ASN][1000 genomes]
rs1768807	0.84[ASN][1000 genomes]
rs1768815	0.84[ASN][1000 genomes]
rs1768817	0.82[ASN][1000 genomes]
rs1768818	0.82[ASN][1000 genomes]
rs2297883	0.84[ASN][1000 genomes]
rs2458400	0.84[ASN][1000 genomes]
rs4660341	0.91[ASN][1000 genomes]
rs7538978	0.83[ASN][1000 genomes]
rs785463	0.84[ASN][1000 genomes]
rs785465	0.84[ASN][1000 genomes]
rs785466	0.84[ASN][1000 genomes]
rs785467	0.84[ASN][1000 genomes]
rs785468	0.84[ASN][1000 genomes]
rs785469	0.84[ASN][1000 genomes]
rs785470	0.84[ASN][1000 genomes]
rs785483	0.88[ASN][1000 genomes]
rs785484	0.91[ASN][1000 genomes]
rs785486	0.91[ASN][1000 genomes]
rs785490	0.91[ASN][1000 genomes]
rs785493	0.91[ASN][1000 genomes]
rs785496	0.91[ASN][1000 genomes]
rs785497	0.91[ASN][1000 genomes]
rs785499	0.88[ASN][1000 genomes]
rs785500	0.88[ASN][1000 genomes]
rs785501	0.80[ASN][1000 genomes]
rs785504	0.96[ASN][1000 genomes]
rs785506	0.85[ASN][1000 genomes]
rs785507	0.85[ASN][1000 genomes]
rs785510	0.84[ASN][1000 genomes]
rs785512	0.84[ASN][1000 genomes]
rs785516	0.88[ASN][1000 genomes]
rs785517	0.91[ASN][1000 genomes]
rs785518	0.83[ASN][1000 genomes]
rs785519	0.91[ASN][1000 genomes]
rs796773	0.90[ASN][1000 genomes]
rs814168	0.84[ASN][1000 genomes]
rs9429095	0.84[ASN][1000 genomes]
rs9429186	0.82[ASN][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	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
2	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
3	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
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1012418	chr1:46544842-46619890	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv534948	chr1:46544842-46619890	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46541200-46595800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:46562400-46595800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:46593200-46595800	Weak transcription	Ovary	ovary
4	chr1:46593400-46598200	Active TSS	Right Atrium	heart
5	chr1:46594000-46599000	Active TSS	Right Ventricle	heart
6	chr1:46594000-46599200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:46594000-46599200	Active TSS	Psoas Muscle	Psoas
8	chr1:46594000-46599400	Active TSS	Left Ventricle	heart
9	chr1:46594200-46595800	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:46594600-46596000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:46594600-46596600	Weak transcription	Placenta	Placenta
12	chr1:46594600-46596800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:46594600-46599200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:46594600-46599400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:46594800-46596200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:46594800-46599200	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr1:46594800-46599400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:46595000-46595400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:46595000-46595800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:46595000-46599200	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr1:46595200-46595400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:46595200-46595400	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr1:46595200-46595400	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr1:46595200-46595400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:46595200-46595400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
26	chr1:46595200-46595400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr1:46595200-46595400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:46595200-46595400	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr1:46595200-46595400	Flanking Active TSS	Fetal Brain Male	brain
30	chr1:46595200-46595400	Flanking Active TSS	Fetal Kidney	kidney
31	chr1:46595200-46595400	Flanking Active TSS	Fetal Lung	lung
32	chr1:46595200-46595400	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr1:46595200-46595400	Flanking Active TSS	HMEC	breast
34	chr1:46595200-46595400	Flanking Active TSS	K562	blood
35	chr1:46595200-46595400	Flanking Active TSS	NH-A	brain
36	chr1:46595200-46595600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:46595200-46595600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:46595200-46595600	Flanking Active TSS	Fetal Brain Female	brain
39	chr1:46595200-46595600	Flanking Active TSS	GM12878-XiMat	blood
40	chr1:46595200-46595600	Flanking Active TSS	Hela-S3	cervix
41	chr1:46595200-46595800	Enhancers	HSMM	muscle
42	chr1:46595200-46596000	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr1:46595200-46596000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
44	chr1:46595200-46596000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
45	chr1:46595200-46596200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:46595200-46596400	Flanking Active TSS	HUVEC	blood vessel
47	chr1:46595200-46596600	Enhancers	Primary T cells from cord blood	blood
48	chr1:46595200-46596600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:46595200-46596600	Bivalent/Poised TSS	Adipose Nuclei	Adipose
50	chr1:46595200-46596800	Flanking Active TSS	Dnd41	blood

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