Variant report

Variant	rs17540171
Chromosome Location	chr15:52301206-52301207
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52300735..52303050-chr15:52304162..52305762,3	MCF-7	breast:
2	chr15:52261811..52265518-chr15:52298759..52302877,5	MCF-7	breast:
3	chr15:52272236..52273812-chr15:52299761..52301744,2	K562	blood:
4	chr15:52273041..52275862-chr15:52300749..52303075,2	MCF-7	breast:
5	chr15:52263196..52265613-chr15:52299179..52302350,3	MCF-7	breast:
6	chr15:52293032..52297316-chr15:52297348..52303144,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166477	Chromatin interaction
ENSG00000069956	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17540734	1.00[AFR][1000 genomes]
rs17612637	1.00[AFR][1000 genomes]
rs17612796	1.00[AFR][1000 genomes]
rs2231289	1.00[AFR][1000 genomes]
rs35581121	1.00[AFR][1000 genomes]
rs41277712	1.00[AFR][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	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1047260	chr15:52257100-52337418	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv1050664	chr15:52265723-52342101	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv517399	chr15:52266878-52305464	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1536	chr15:52276293-52320919	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52293000-52303200	Weak transcription	Pancreas	Pancrea
2	chr15:52293400-52303200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:52296600-52303400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:52297600-52301600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr15:52297800-52301400	Enhancers	HepG2	liver
6	chr15:52297800-52301600	Enhancers	Stomach Mucosa	stomach
7	chr15:52297800-52301800	Enhancers	Primary B cells from peripheral blood	blood
8	chr15:52297800-52304400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:52298400-52301600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr15:52298400-52302400	Enhancers	K562	blood
11	chr15:52299000-52304200	Weak transcription	Psoas Muscle	Psoas
12	chr15:52299200-52301400	Enhancers	Placenta	Placenta
13	chr15:52299200-52304200	Weak transcription	Fetal Heart	heart
14	chr15:52299400-52301600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr15:52299400-52301800	Enhancers	HUVEC	blood vessel
16	chr15:52299400-52303000	Weak transcription	HSMM	muscle
17	chr15:52299400-52303200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:52299400-52303200	Weak transcription	NHDF-Ad	bronchial
19	chr15:52299400-52303200	Weak transcription	NHLF	lung
20	chr15:52299400-52310800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:52299600-52301400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:52299600-52301400	Weak transcription	Fetal Intestine Large	intestine
23	chr15:52299600-52302200	Weak transcription	NHEK	skin
24	chr15:52299600-52302800	Weak transcription	HMEC	breast
25	chr15:52299600-52303000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:52299600-52303000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:52299600-52303000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:52299600-52303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:52299600-52303000	Weak transcription	NH-A	brain
30	chr15:52299600-52303000	Weak transcription	Osteobl	bone
31	chr15:52299600-52303200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:52299600-52303200	Weak transcription	Right Atrium	heart
33	chr15:52299600-52303400	Weak transcription	Esophagus	oesophagus
34	chr15:52299600-52303400	Weak transcription	Left Ventricle	heart
35	chr15:52299600-52304000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:52299600-52305400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr15:52299600-52305600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:52299600-52310200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:52299600-52310600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:52299600-52310800	Weak transcription	HSMMtube	muscle
41	chr15:52299800-52303200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr15:52300200-52301400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:52300200-52301400	Enhancers	Spleen	Spleen
44	chr15:52300200-52301600	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr15:52300200-52301600	Enhancers	Adipose Nuclei	Adipose
46	chr15:52300400-52301400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr15:52300400-52301400	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr15:52300400-52301600	Flanking Active TSS	GM12878-XiMat	blood
49	chr15:52300400-52301600	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr15:52300400-52301800	Enhancers	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links