Variant report

Variant	rs7175663
Chromosome Location	chr15:52572875-52572876
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr15:52572298-52572916	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYBL2	chr15:52572804-52573779	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52567021..52571873-chr15:52572571..52576998,5	MCF-7	breast:
2	chr15:52572320..52574802-chr15:52575555..52577846,2	MCF-7	breast:
3	chr15:52564168..52566004-chr15:52571298..52572896,2	MCF-7	breast:
4	chr15:52541572..52560373-chr15:52569752..52591000,64	MCF-7	breast:

Variant related genes	Relation type
MIR1266	TF binding region
ENSG00000128833	Chromatin interaction
ENSG00000221052	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs17650694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17707007	1.00[MEX][hapmap]
rs28679378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28776010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41504447	1.00[MEX][hapmap]
rs4268699	1.00[MEX][hapmap]
rs7161988	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7162229	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7175545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73406657	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52524400-52579400	Weak transcription	Small Intestine	intestine
2	chr15:52550000-52579200	Weak transcription	Fetal Kidney	kidney
3	chr15:52553200-52575400	Strong transcription	Rectal Mucosa Donor 31	rectum
4	chr15:52554800-52582200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:52555000-52585000	Weak transcription	Left Ventricle	heart
6	chr15:52555200-52580600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:52555400-52574400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:52555400-52575800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:52555800-52573400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr15:52555800-52574000	Weak transcription	Brain Anterior Caudate	brain
11	chr15:52555800-52575800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:52555800-52576400	Weak transcription	Hela-S3	cervix
13	chr15:52556000-52587000	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:52557000-52575800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:52558200-52575400	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr15:52558800-52579400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:52559000-52573400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr15:52559200-52573800	Weak transcription	Esophagus	oesophagus
19	chr15:52559400-52580600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:52561400-52580600	Weak transcription	Spleen	Spleen
21	chr15:52563800-52575000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr15:52564400-52575800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:52565000-52575000	Strong transcription	Fetal Stomach	stomach
24	chr15:52565800-52587000	Weak transcription	Right Atrium	heart
25	chr15:52567200-52573400	Strong transcription	Fetal Intestine Large	intestine
26	chr15:52567200-52575800	Strong transcription	Fetal Intestine Small	intestine
27	chr15:52568600-52576400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr15:52568600-52579400	Weak transcription	Stomach Mucosa	stomach
29	chr15:52568800-52580000	Weak transcription	Colonic Mucosa	Colon
30	chr15:52570200-52573000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:52570600-52573400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:52570600-52573400	Weak transcription	Fetal Brain Female	brain
33	chr15:52570800-52573600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:52570800-52580800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:52571200-52581000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:52571200-52585800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr15:52571200-52587000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:52571400-52580600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr15:52571400-52580600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr15:52571600-52573200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:52571600-52573600	Weak transcription	A549	lung
42	chr15:52571600-52579200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr15:52571600-52579200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:52571800-52573800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:52571800-52574400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:52571800-52574800	Weak transcription	Adipose Nuclei	Adipose
47	chr15:52572200-52573400	Weak transcription	Fetal Muscle Leg	muscle
48	chr15:52572200-52573400	Weak transcription	Gastric	stomach
49	chr15:52572200-52574200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr15:52572200-52575800	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links