Variant report

Variant	rs2420373
Chromosome Location	chr1:169498181-169498182
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:169471872..169473392-chr1:169496086..169498392,2	MCF-7	breast:
2	chr1:169447411..169449419-chr1:169497697..169499792,2	MCF-7	breast:
3	chr1:169478952..169480932-chr1:169498032..169500995,2	MCF-7	breast:
4	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
5	chr1:169490192..169493609-chr1:169495804..169500257,7	MCF-7	breast:
6	chr1:169485353..169488291-chr1:169497708..169499497,2	K562	blood:
7	chr1:169475721..169488506-chr1:169493331..169501885,21	MCF-7	breast:
8	chr1:169463786..169466732-chr1:169496061..169498768,2	MCF-7	breast:
9	chr1:169464842..169466756-chr1:169497919..169499478,2	MCF-7	breast:
10	chr1:169452411..169456753-chr1:169494976..169501006,10	MCF-7	breast:
11	chr1:169480009..169482936-chr1:169495810..169499823,3	K562	blood:
12	chr1:169454264..169456422-chr1:169495447..169500944,4	K562	blood:
13	chr1:169460825..169464071-chr1:169495499..169498354,3	MCF-7	breast:
14	chr1:169461099..169462759-chr1:169496804..169499532,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213062	Chromatin interaction
ENSG00000117479	Chromatin interaction
ENSG00000198734	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10800450	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10800453	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10919178	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1121789	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11579441	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12127364	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2009814	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2187952	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2187953	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2213866	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2213867	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2227244	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2239851	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3766109	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4524	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4525	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4656187	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4656684	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4656685	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6016	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6017	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6021	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6030	0.88[AFR][1000 genomes]
rs6032	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6662593	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6662696	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6670393	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6675244	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9287090	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9287092	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9332600	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9332619	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332620	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332627	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332635	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9332643	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9332651	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332655	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9332667	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs970741	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs974793	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv872533	chr1:169490401-169508576	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169484800-169501000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:169485400-169510600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:169487400-169501000	Weak transcription	Right Ventricle	heart
4	chr1:169491600-169500800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:169492000-169499800	Weak transcription	Left Ventricle	heart
6	chr1:169494000-169502800	Strong transcription	HepG2	liver
7	chr1:169494800-169499200	Enhancers	Stomach Mucosa	stomach
8	chr1:169495200-169498600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:169495400-169498200	Weak transcription	Hela-S3	cervix
10	chr1:169496000-169499200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:169496000-169515200	Strong transcription	Liver	Liver
12	chr1:169496200-169498400	Enhancers	Placenta	Placenta
13	chr1:169496200-169499000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr1:169496200-169499000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr1:169496400-169498200	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr1:169496400-169499000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
17	chr1:169496600-169498400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr1:169496600-169498400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:169496800-169498400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:169496800-169498600	Enhancers	Thymus	Thymus
21	chr1:169496800-169498600	Genic enhancers	Monocytes-CD14+_RO01746	blood
22	chr1:169496800-169498800	Genic enhancers	Primary monocytes fromperipheralblood	blood
23	chr1:169496800-169500000	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:169497000-169498200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr1:169497000-169498200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr1:169497000-169498400	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr1:169497000-169498600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:169497000-169498600	Enhancers	HMEC	breast
29	chr1:169497000-169499000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:169497000-169499000	Enhancers	Fetal Thymus	thymus
31	chr1:169497200-169498200	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr1:169497200-169498600	Enhancers	GM12878-XiMat	blood
33	chr1:169497200-169498800	Enhancers	K562	blood
34	chr1:169497200-169499200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr1:169497200-169499400	Enhancers	Fetal Intestine Large	intestine
36	chr1:169497200-169499600	Enhancers	Dnd41	blood
37	chr1:169497200-169500000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:169497400-169498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:169497400-169498400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:169497600-169498600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:169497600-169498600	Weak transcription	HSMMtube	muscle
42	chr1:169497600-169499800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:169497800-169498200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:169497800-169498400	Enhancers	Primary T cells from cord blood	blood
45	chr1:169497800-169498400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
46	chr1:169497800-169498400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:169498000-169498200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr1:169498000-169498200	Active TSS	Primary B cells from cord blood	blood
49	chr1:169498000-169498200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr1:169498000-169498400	Flanking Active TSS	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links