Variant report

Variant	rs12562646
Chromosome Location	chr1:227155481-227155482
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227154071..227157064-chr1:227173659..227175478,2	MCF-7	breast:
2	chr1:227127006..227129793-chr1:227152681..227157136,4	K562	blood:
3	chr1:227155411..227157557-chr1:227159728..227161505,2	MCF-7	breast:
4	chr1:227154208..227155807-chr1:227178549..227181040,2	K562	blood:
5	chr1:227127006..227129675-chr1:227153566..227157136,5	K562	blood:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction
ENSG00000233706	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12562621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12565025	1.00[ASN][1000 genomes]
rs12565212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12565685	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12567464	0.89[CHB][hapmap];0.92[ASN][1000 genomes]
rs12567790	0.92[ASN][1000 genomes]
rs12567972	0.88[ASN][1000 genomes]
rs12568014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1316851	0.89[CHB][hapmap];0.92[ASN][1000 genomes]
rs16841298	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16846716	0.89[CHB][hapmap];0.92[ASN][1000 genomes]
rs16846731	0.89[CHB][hapmap];0.92[ASN][1000 genomes]
rs16846733	0.89[CHB][hapmap];0.92[ASN][1000 genomes]
rs16846735	0.85[ASN][1000 genomes]
rs16846738	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16846751	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16846772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16846779	0.92[ASN][1000 genomes]
rs16846780	0.92[ASN][1000 genomes]
rs16846783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16846790	0.88[ASN][1000 genomes]
rs16846792	0.88[ASN][1000 genomes]
rs16846798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16846808	0.92[ASN][1000 genomes]
rs16846811	0.92[ASN][1000 genomes]
rs16846903	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs16846944	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs16847001	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs16847020	0.89[CHB][hapmap]
rs2009053	0.92[ASN][1000 genomes]
rs2297411	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2297417	0.92[ASN][1000 genomes]
rs3738728	0.88[ASN][1000 genomes]
rs3795450	0.92[ASN][1000 genomes]
rs3795452	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs41527149	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4281295	0.92[ASN][1000 genomes]
rs4459073	0.92[ASN][1000 genomes]
rs4521963	0.92[ASN][1000 genomes]
rs56043893	0.92[ASN][1000 genomes]
rs60107850	1.00[ASN][1000 genomes]
rs944601	0.89[CHB][hapmap];0.92[ASN][1000 genomes]
rs944602	0.89[CHB][hapmap];0.92[ASN][1000 genomes]
rs961490	0.84[ASN][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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
3	nsv873236	chr1:227118912-227173537	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv873237	chr1:227118912-227178948	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv873238	chr1:227118912-227180858	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv520923	chr1:227127618-227178948	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227129000-227162600	Weak transcription	Fetal Kidney	kidney
2	chr1:227131000-227171800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:227135200-227158000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:227142200-227157800	Weak transcription	Fetal Lung	lung
5	chr1:227143400-227161200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:227145400-227159600	Weak transcription	Brain Substantia Nigra	brain
7	chr1:227146400-227162600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:227147000-227177000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:227147200-227161000	Weak transcription	Stomach Mucosa	stomach
10	chr1:227147400-227156400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:227147800-227158600	Strong transcription	Primary T cells from cord blood	blood
12	chr1:227148200-227162000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:227148400-227156400	Strong transcription	Fetal Intestine Small	intestine
14	chr1:227148400-227156600	Strong transcription	Fetal Stomach	stomach
15	chr1:227148400-227159400	Weak transcription	A549	lung
16	chr1:227148600-227158400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:227148600-227180800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:227149000-227157600	Weak transcription	K562	blood
19	chr1:227149000-227158600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:227149200-227156600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:227149200-227158400	Strong transcription	Ovary	ovary
22	chr1:227149400-227156400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:227149400-227158400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:227149400-227161600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:227150000-227155800	Genic enhancers	Left Ventricle	heart
26	chr1:227150200-227158400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr1:227150400-227158000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:227150400-227159600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:227150800-227159400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:227151200-227158000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:227151200-227158200	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr1:227151400-227159400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:227151800-227159400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:227152000-227156200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:227152000-227156800	Strong transcription	Fetal Intestine Large	intestine
36	chr1:227152200-227159400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr1:227152400-227155600	Strong transcription	Spleen	Spleen
38	chr1:227152400-227155800	Strong transcription	Adipose Nuclei	Adipose
39	chr1:227152400-227155800	Strong transcription	Lung	lung
40	chr1:227152400-227157800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:227152400-227159000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr1:227152400-227160600	Weak transcription	Small Intestine	intestine
43	chr1:227152400-227161800	Weak transcription	HSMMtube	muscle
44	chr1:227152600-227157600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:227152800-227158400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr1:227152800-227160600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:227153000-227155600	Strong transcription	HepG2	liver
48	chr1:227153000-227156000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:227153000-227160600	Weak transcription	Fetal Heart	heart
50	chr1:227153200-227156000	Strong transcription	Rectal Mucosa Donor 31	rectum

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