Variant report

Variant	rs627458
Chromosome Location	chr15:41197736-41197737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41197521-41198057	HepG2	liver:	n/a	n/a
2	HCFC1	chr15:41197576-41199994	Hela-S3	cervix:	n/a	n/a
3	SMC3	chr15:41197733-41199318	SK-N-SH	brain:	n/a	chr15:41198713-41198727 chr15:41199116-41199130

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41186236..41188043-chr15:41197568..41199237,2	MCF-7	breast:
2	chr15:41196932..41200984-chr15:41244050..41248455,6	K562	blood:
3	chr15:41195887..41198690-chr15:41257429..41259190,2	K562	blood:
4	chr15:41195189..41208751-chr15:41218816..41225232,20	MCF-7	breast:
5	chr15:41195654..41197796-chr15:41319760..41321629,2	K562	blood:
6	chr15:41197462..41204234-chr15:41215803..41223321,13	K562	blood:
7	chr15:41194927..41205036-chr15:41218861..41227276,20	MCF-7	breast:
8	chr15:41162876..41167684-chr15:41196844..41200482,5	MCF-7	breast:
9	chr15:41136563..41138261-chr15:41195693..41197954,2	MCF-7	breast:
10	chr15:41189733..41192920-chr15:41195198..41198883,3	MCF-7	breast:
11	chr15:41196932..41198617-chr15:41624886..41627163,2	K562	blood:
12	chr15:41135781..41139367-chr15:41195514..41200270,4	MCF-7	breast:
13	chr15:41193987..41204234-chr15:41215915..41223506,12	K562	blood:
14	chr15:41196932..41198542-chr15:41624886..41626629,2	K562	blood:
15	chr15:41196697..41198926-chr15:41308162..41310541,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000251161	TF binding region
ENSG00000261183	Chromatin interaction
ENSG00000104140	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000128965	Chromatin interaction
ENSG00000137804	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000259521	Chromatin interaction
ENSG00000264256	Chromatin interaction
ENSG00000128917	Chromatin interaction
ENSG00000128908	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2008102	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3100812	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs604751	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs611694	0.81[AFR][1000 genomes]
rs9806683	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv904104	chr15:41149824-41234932	Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
7	esv1819792	chr15:41184722-41234825	Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41188200-41197800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr15:41188200-41198000	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr15:41188200-41198800	Weak transcription	Small Intestine	intestine
4	chr15:41188400-41197800	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr15:41188400-41198000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:41188400-41198000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:41189800-41198200	Strong transcription	Fetal Brain Female	brain
8	chr15:41193200-41198000	Weak transcription	Psoas Muscle	Psoas
9	chr15:41193600-41198200	Weak transcription	K562	blood
10	chr15:41194800-41198000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:41195400-41198400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:41195600-41198800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:41195800-41198000	Genic enhancers	NHLF	lung
14	chr15:41195800-41198600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr15:41195800-41198800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:41195800-41198800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:41196000-41198200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:41196000-41198600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:41196000-41198800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr15:41196200-41197800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:41196200-41197800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr15:41196200-41197800	Weak transcription	NHDF-Ad	bronchial
23	chr15:41196200-41198000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr15:41196200-41198000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr15:41196200-41198000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:41196200-41198200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:41196200-41198200	Enhancers	Duodenum Mucosa	Duodenum
28	chr15:41196200-41198600	Enhancers	Primary B cells from peripheral blood	blood
29	chr15:41196200-41198600	Weak transcription	Ovary	ovary
30	chr15:41196200-41198800	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr15:41196200-41198800	Weak transcription	Fetal Kidney	kidney
32	chr15:41196400-41197800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:41196400-41197800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:41196400-41197800	Weak transcription	Brain Anterior Caudate	brain
35	chr15:41196400-41197800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr15:41196400-41197800	Weak transcription	Brain Substantia Nigra	brain
37	chr15:41196400-41197800	Weak transcription	Right Atrium	heart
38	chr15:41196400-41197800	Weak transcription	Right Ventricle	heart
39	chr15:41196400-41197800	Weak transcription	Stomach Mucosa	stomach
40	chr15:41196400-41197800	Weak transcription	Spleen	Spleen
41	chr15:41196400-41198000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:41196400-41198000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr15:41196400-41198000	Weak transcription	NHEK	skin
44	chr15:41196400-41198200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr15:41196400-41198200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr15:41196400-41198200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr15:41196400-41198200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:41196400-41198200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:41196400-41198200	Weak transcription	HMEC	breast
50	chr15:41196400-41198200	Genic enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links