Variant report

Variant	rs41269079
Chromosome Location	chr1:45252015-45252016
allele	A/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	chr1:45248852..45254229-chr1:45263166..45267959,10	MCF-7	breast:
2	chr1:45194298..45199848-chr1:45247467..45253056,11	MCF-7	breast:
3	chr1:45251857..45252388-chr1:45301281..45302200,2	K562	blood:
4	chr1:45249665..45252249-chr1:45973205..45975884,2	K562	blood:
5	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
6	chr1:45248546..45252735-chr1:45278815..45281288,3	MCF-7	breast:
7	chr1:45250617..45252032-chr1:45769367..45770140,3	K562	blood:
8	chr1:45246681..45259677-chr1:45281336..45290057,25	MCF-7	breast:
9	chr1:45248330..45252127-chr1:45262500..45268022,8	MCF-7	breast:
10	chr1:45186774..45188887-chr1:45250601..45252692,2	MCF-7	breast:
11	chr1:45194501..45200206-chr1:45249194..45253143,8	MCF-7	breast:
12	chr1:45248400..45253844-chr1:45268438..45273783,8	MCF-7	breast:
13	chr1:45251452..45252216-chr1:45765452..45766253,2	K562	blood:
14	chr1:45248466..45253060-chr1:45282997..45288611,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000188396	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000173846	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12057238	0.92[ASN][1000 genomes]
rs12057414	0.99[ASN][1000 genomes]
rs12402781	0.92[ASN][1000 genomes]
rs12404160	0.85[ASN][1000 genomes]
rs12407290	0.90[ASN][1000 genomes]
rs12407627	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17391430	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17883304	0.90[ASN][1000 genomes]
rs17885815	0.85[ASN][1000 genomes]
rs3795712	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3795715	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806398	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923304	0.90[ASN][1000 genomes]
rs4520451	0.85[ASN][1000 genomes]
rs4565758	0.90[ASN][1000 genomes]
rs55703843	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58532407	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58603818	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59895800	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60452778	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60766209	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72674017	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72674023	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
8	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
10	nsv947252	chr1:45242176-45258816	Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45245000-45258600	Weak transcription	Hela-S3	cervix
2	chr1:45249200-45252600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:45250200-45253200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:45250400-45252600	Enhancers	Placenta Amnion	Placenta Amnion
5	chr1:45251200-45252400	Enhancers	Gastric	stomach
6	chr1:45251200-45252400	Flanking Active TSS	GM12878-XiMat	blood
7	chr1:45251400-45252200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:45251400-45252200	Flanking Active TSS	NH-A	brain
9	chr1:45251400-45252200	Flanking Active TSS	NHEK	skin
10	chr1:45251400-45252400	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr1:45251400-45252400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
12	chr1:45251400-45252600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr1:45251400-45252600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:45251400-45252600	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr1:45251600-45252200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:45251600-45252200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:45251600-45252200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:45251600-45252200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr1:45251600-45252200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:45251600-45252200	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr1:45251600-45252200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr1:45251600-45252200	Enhancers	Small Intestine	intestine
23	chr1:45251600-45252200	Flanking Active TSS	Thymus	Thymus
24	chr1:45251600-45252200	Flanking Active TSS	Osteobl	bone
25	chr1:45251600-45252400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr1:45251600-45252400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:45251600-45252400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:45251600-45252400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:45251600-45252400	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr1:45251600-45252400	Flanking Active TSS	Liver	Liver
31	chr1:45251600-45252400	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr1:45251600-45252400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr1:45251600-45252400	Flanking Active TSS	Fetal Intestine Large	intestine
34	chr1:45251600-45252400	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr1:45251600-45252400	Flanking Active TSS	Fetal Muscle Leg	muscle
36	chr1:45251600-45252400	Flanking Active TSS	Fetal Thymus	thymus
37	chr1:45251600-45252400	Enhancers	Lung	lung
38	chr1:45251600-45252400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr1:45251600-45252400	Active TSS	Right Ventricle	heart
40	chr1:45251600-45252400	Flanking Active TSS	HUVEC	blood vessel
41	chr1:45251600-45252600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr1:45251600-45252600	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr1:45251600-45252600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr1:45251600-45252600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr1:45251600-45252600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr1:45251600-45252600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:45251600-45252600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:45251600-45252600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:45251600-45252600	Flanking Active TSS	Colonic Mucosa	Colon
50	chr1:45251600-45252600	Flanking Active TSS	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links