Variant report

Variant	rs28525101
Chromosome Location	chr17:16570067-16570068
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16555258..16557241-chr17:16567702..16570087,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264765	Chromatin interaction
ENSG00000197566	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1005369	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1005370	0.81[ASN][1000 genomes]
rs12103873	0.90[EUR][1000 genomes]
rs16959857	0.81[ASN][1000 genomes]
rs16959869	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16959870	0.81[ASN][1000 genomes]
rs28398264	0.93[EUR][1000 genomes]
rs28431824	0.82[ASN][1000 genomes]
rs28458310	0.82[ASN][1000 genomes]
rs28458353	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28525658	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28526077	0.95[EUR][1000 genomes]
rs28626982	0.82[ASN][1000 genomes]
rs28636605	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28674185	0.82[ASN][1000 genomes]
rs28751872	0.82[ASN][1000 genomes]
rs28754336	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28792801	0.81[ASN][1000 genomes]
rs28826699	0.81[ASN][1000 genomes]
rs28865976	0.81[ASN][1000 genomes]
rs28875211	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3813762	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4352086	0.82[ASN][1000 genomes]
rs4791672	0.80[ASN][1000 genomes]
rs4791673	0.81[ASN][1000 genomes]
rs4791676	0.82[ASN][1000 genomes]
rs4791678	0.82[ASN][1000 genomes]
rs4792757	0.81[ASN][1000 genomes]
rs4792760	0.81[ASN][1000 genomes]
rs4792761	0.82[ASN][1000 genomes]
rs4792762	0.82[ASN][1000 genomes]
rs5000166	0.82[ASN][1000 genomes]
rs56303920	0.82[ASN][1000 genomes]
rs57448521	0.81[ASN][1000 genomes]
rs58164310	0.82[ASN][1000 genomes]
rs59486407	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59594997	0.82[ASN][1000 genomes]
rs59826203	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62072781	0.81[ASN][1000 genomes]
rs62072792	0.81[ASN][1000 genomes]
rs62072845	0.80[ASN][1000 genomes]
rs62073660	0.81[ASN][1000 genomes]
rs6502514	0.81[ASN][1000 genomes]
rs7208075	0.82[ASN][1000 genomes]
rs7213274	0.82[ASN][1000 genomes]
rs7217544	0.81[ASN][1000 genomes]
rs7217717	0.81[ASN][1000 genomes]
rs7218241	0.82[ASN][1000 genomes]
rs7219632	0.81[ASN][1000 genomes]
rs7221518	0.82[ASN][1000 genomes]
rs7222875	0.82[ASN][1000 genomes]
rs7225641	0.82[ASN][1000 genomes]
rs72637356	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72637357	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72637358	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72637359	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72637360	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72637361	0.88[EUR][1000 genomes]
rs72637362	0.90[EUR][1000 genomes]
rs72637363	0.93[EUR][1000 genomes]
rs8065558	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8068349	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8074285	0.81[ASN][1000 genomes]
rs8074464	0.81[ASN][1000 genomes]
rs8074487	0.82[ASN][1000 genomes]
rs8075988	0.81[ASN][1000 genomes]
rs8076849	0.82[ASN][1000 genomes]
rs8082225	0.89[EUR][1000 genomes]
rs8082650	0.82[ASN][1000 genomes]
rs9889227	0.81[ASN][1000 genomes]
rs9890123	0.81[ASN][1000 genomes]
rs9890698	0.81[ASN][1000 genomes]
rs9891138	0.81[ASN][1000 genomes]
rs9894637	0.81[ASN][1000 genomes]
rs9898888	0.90[EUR][1000 genomes]
rs9899785	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9899919	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9904901	0.81[ASN][1000 genomes]
rs9905710	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9906261	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9906728	0.81[ASN][1000 genomes]
rs9907785	0.81[ASN][1000 genomes]
rs9908015	0.82[ASN][1000 genomes]
rs9908390	0.82[ASN][1000 genomes]
rs9909044	0.81[ASN][1000 genomes]
rs9909955	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9910087	0.81[ASN][1000 genomes]
rs9910842	0.82[ASN][1000 genomes]
rs9911162	0.82[ASN][1000 genomes]
rs9911524	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9911608	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9911820	0.82[ASN][1000 genomes]
rs9911851	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9915121	0.90[EUR][1000 genomes]
rs9916069	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9916258	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9916464	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
2	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
3	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv2758442	chr17:16527056-16817437	Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv2758676	chr17:16527056-16817437	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv427991	chr17:16527056-16817437	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv907720	chr17:16557606-16758204	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv978372	chr17:16559570-16587380	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv962373	chr17:16568919-16576327	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16569600-16571000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr17:16569800-16570600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
3	chr17:16570000-16570200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:16570000-16570200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr17:16570000-16570200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr17:16570000-16570200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
7	chr17:16570000-16570200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr17:16570000-16570200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr17:16570000-16570200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:16570000-16570200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
11	chr17:16570000-16570200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr17:16570000-16570200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr17:16570000-16570200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr17:16570000-16570200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr17:16570000-16570200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
16	chr17:16570000-16570200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr17:16570000-16570200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr17:16570000-16570200	Bivalent Enhancer	Fetal Stomach	stomach
19	chr17:16570000-16570200	Enhancers	Gastric	stomach
20	chr17:16570000-16570200	Flanking Active TSS	Right Ventricle	heart
21	chr17:16570000-16570200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
22	chr17:16570000-16570400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr17:16570000-16570400	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
24	chr17:16570000-16570400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
25	chr17:16570000-16570400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr17:16570000-16570400	Bivalent/Poised TSS	Left Ventricle	heart
27	chr17:16570000-16570400	Enhancers	Pancreas	Pancrea
28	chr17:16570000-16570400	Active TSS	Right Atrium	heart
29	chr17:16570000-16570400	Bivalent Enhancer	Spleen	Spleen
30	chr17:16570000-16570600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr17:16570000-16570600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr17:16570000-16570600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
33	chr17:16570000-16570600	Enhancers	Liver	Liver
34	chr17:16570000-16570600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
35	chr17:16570000-16570800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
36	chr17:16570000-16570800	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
37	chr17:16570000-16570800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
38	chr17:16570000-16570800	Flanking Bivalent TSS/Enh	HMEC	breast
39	chr17:16570000-16571000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
40	chr17:16570000-16571000	Active TSS	H9 Cell Line	embryonic stem cell
41	chr17:16570000-16571000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr17:16570000-16571000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr17:16570000-16571000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr17:16570000-16571000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr17:16570000-16571000	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr17:16570000-16571000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr17:16570000-16571000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
48	chr17:16570000-16571000	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
49	chr17:16570000-16571000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr17:16570000-16571000	Active TSS	Brain Angular Gyrus	brain

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