Variant report

Variant	rs57011078
Chromosome Location	chr1:154196241-154196242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154196035-154196841	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr1:154195513-154196668	MCF10A-Er-Src	breast:	n/a	n/a
3	IRF1	chr1:154196202-154196453	K562	blood:	n/a	chr1:154196278-154196287
4	POLR2A	chr1:154196178-154197163	K562	blood:	n/a	n/a
5	SPI1	chr1:154196080-154196498	HL-60	blood:	n/a	n/a
6	POLR2A	chr1:154195548-154196373	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154194303..154196479-chr1:154230537..154232056,2	MCF-7	breast:
2	chr1:153916668..153920266-chr1:154191885..154196472,6	MCF-7	breast:
3	chr1:154196164..154196918-chr4:37248947..37249743,2	MCF-7	breast:
4	chr1:154193867..154196410-chr1:154304631..154306238,2	K562	blood:
5	chr1:154161421..154168420-chr1:154191340..154198003,13	MCF-7	breast:
6	chr1:154196196..154198596-chr1:154226776..154229363,3	K562	blood:
7	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:
8	chr1:154195913..154198851-chr1:154227024..154228949,3	K562	blood:
9	chr1:154190796..154197109-chr1:154207892..154217963,21	MCF-7	breast:
10	chr1:154195648..154197587-chr1:154233739..154236534,2	MCF-7	breast:
11	chr1:154177747..154182716-chr1:154190412..154196946,9	K562	blood:
12	chr1:154171859..154174380-chr1:154194428..154197108,2	MCF-7	breast:

No data

Variant related genes	Relation type
UBAP2L	TF binding region
C1orf43	TF binding region
ENSG00000143549	Chromatin interaction
ENSG00000198837	Chromatin interaction
ENSG00000163263	Chromatin interaction
ENSG00000252817	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000215938	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1194597	0.87[AMR][1000 genomes]
rs1194601	0.85[AFR][1000 genomes]
rs1194605	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1205590	0.84[AFR][1000 genomes]
rs1760791	0.87[AFR][1000 genomes]
rs2500222	1.00[AMR][1000 genomes]
rs55650526	0.87[AMR][1000 genomes]
rs55857358	0.86[AFR][1000 genomes]
rs56752149	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs56760430	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs59651124	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60506384	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs60743909	0.83[AFR][1000 genomes];0.87[AMR][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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription 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 miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154194400-154197400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:154194400-154197600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:154194600-154196600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:154194600-154196600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
5	chr1:154194600-154197200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:154194600-154197400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr1:154194600-154197600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:154194600-154197600	Weak transcription	Gastric	stomach
9	chr1:154194600-154197600	Weak transcription	Spleen	Spleen
10	chr1:154194600-154199600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:154194600-154201000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:154194600-154201000	Weak transcription	Aorta	Aorta
13	chr1:154194600-154201000	Weak transcription	Esophagus	oesophagus
14	chr1:154194600-154201000	Weak transcription	Pancreas	Pancrea
15	chr1:154194800-154197600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:154194800-154197600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:154194800-154197600	Weak transcription	Lung	lung
18	chr1:154194800-154197800	Weak transcription	Placenta	Placenta
19	chr1:154194800-154197800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:154194800-154198000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:154194800-154198600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:154194800-154199200	Weak transcription	Left Ventricle	heart
23	chr1:154194800-154199400	Weak transcription	Small Intestine	intestine
24	chr1:154194800-154202000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:154195000-154196400	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr1:154195000-154196400	Enhancers	Fetal Heart	heart
27	chr1:154195000-154196800	Enhancers	Fetal Intestine Large	intestine
28	chr1:154195000-154197000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:154195000-154197000	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr1:154195000-154197000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr1:154195000-154197200	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr1:154195000-154197800	Weak transcription	Brain Substantia Nigra	brain
33	chr1:154195200-154196400	Enhancers	Adipose Nuclei	Adipose
34	chr1:154195200-154196400	Weak transcription	Brain Angular Gyrus	brain
35	chr1:154195200-154196400	Enhancers	Brain Anterior Caudate	brain
36	chr1:154195200-154196600	Weak transcription	Fetal Brain Female	brain
37	chr1:154195200-154196800	Enhancers	Fetal Kidney	kidney
38	chr1:154195200-154196800	Genic enhancers	NHEK	skin
39	chr1:154195200-154197000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:154195200-154197000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:154195200-154197000	Enhancers	Liver	Liver
42	chr1:154195200-154197200	Enhancers	Rectal Smooth Muscle	rectum
43	chr1:154195200-154197400	Enhancers	Brain Cingulate Gyrus	brain
44	chr1:154195200-154197600	Weak transcription	Ovary	ovary
45	chr1:154195200-154197600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:154195200-154197800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:154195200-154197800	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:154195200-154198000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:154195200-154199200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:154195200-154199400	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links