Variant report

Variant	rs859260
Chromosome Location	chr17:15820665-15820666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:15819602..15821859-chr17:15822735..15824245,2	MCF-7	breast:
2	chr17:15820333..15822975-chr17:15833482..15836087,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1102644	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868331	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11868613	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11869184	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11872072	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1622059	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1622062	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1797463	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2058366	1.00[EUR][1000 genomes]
rs2482988	1.00[EUR][1000 genomes]
rs2535600	1.00[EUR][1000 genomes]
rs2535602	1.00[EUR][1000 genomes]
rs2535604	1.00[EUR][1000 genomes]
rs2779190	1.00[EUR][1000 genomes]
rs2779191	1.00[EUR][1000 genomes]
rs2779194	1.00[EUR][1000 genomes]
rs2779203	1.00[EUR][1000 genomes]
rs3859259	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4791645	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4791646	1.00[EUR][1000 genomes]
rs4791651	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4791654	1.00[EUR][1000 genomes]
rs4792695	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4792696	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4792697	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4792698	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs484520	1.00[EUR][1000 genomes]
rs500752	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs513190	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs708592	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7209188	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs758854	1.00[EUR][1000 genomes]
rs758855	1.00[EUR][1000 genomes]
rs758856	1.00[EUR][1000 genomes]
rs8079191	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs859225	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859227	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs859231	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859239	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs859241	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859242	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859244	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859245	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859246	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs859249	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859250	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859251	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859254	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859258	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859259	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859261	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859262	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859263	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859264	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859265	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859266	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859267	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859268	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers 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	190 gene(s)	inside rSNPs	diseases
4	nsv1062951	chr17:15561070-15890644	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1066023	chr17:15607267-16053512	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
7	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
8	nsv1061222	chr17:15672934-15999778	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
9	nsv907706	chr17:15731923-16056442	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv1067555	chr17:15804228-16001117	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
12	nsv1061987	chr17:15810017-15855135	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15809800-15820800	Weak transcription	Gastric	stomach
2	chr17:15812000-15820800	Weak transcription	Left Ventricle	heart
3	chr17:15813400-15820800	Weak transcription	Pancreas	Pancrea
4	chr17:15814600-15822400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr17:15816200-15820800	Weak transcription	Fetal Heart	heart
6	chr17:15816200-15820800	Weak transcription	Right Atrium	heart
7	chr17:15816600-15820800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr17:15817200-15825000	Enhancers	Hela-S3	cervix
9	chr17:15818600-15823800	Weak transcription	Placenta	Placenta
10	chr17:15820200-15820800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr17:15820400-15821200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
12	chr17:15820400-15821400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr17:15820400-15821400	Enhancers	Esophagus	oesophagus
14	chr17:15820400-15821400	Bivalent Enhancer	Fetal Intestine Small	intestine
15	chr17:15820400-15824400	Weak transcription	HUVEC	blood vessel
16	chr17:15820600-15820800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr17:15820600-15820800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr17:15820600-15820800	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr17:15820600-15820800	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr17:15820600-15820800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr17:15820600-15820800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
22	chr17:15820600-15820800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr17:15820600-15820800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
24	chr17:15820600-15820800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
25	chr17:15820600-15820800	Bivalent Enhancer	Fetal Muscle Leg	muscle
26	chr17:15820600-15820800	Bivalent Enhancer	Fetal Stomach	stomach
27	chr17:15820600-15820800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr17:15820600-15820800	Bivalent Enhancer	Psoas Muscle	Psoas
29	chr17:15820600-15821000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr17:15820600-15821000	Enhancers	NHDF-Ad	bronchial
31	chr17:15820600-15821000	Flanking Active TSS	Osteobl	bone
32	chr17:15820600-15821200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr17:15820600-15821200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr17:15820600-15821200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr17:15820600-15821200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
36	chr17:15820600-15821200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
37	chr17:15820600-15821200	Flanking Active TSS	Right Ventricle	heart
38	chr17:15820600-15821200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
39	chr17:15820600-15821400	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr17:15820600-15821400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr17:15820600-15821400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
42	chr17:15820600-15821400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:15820600-15821400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr17:15820600-15821400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr17:15820600-15821400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr17:15820600-15821400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr17:15820600-15821400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr17:15820600-15821400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
49	chr17:15820600-15821400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr17:15820600-15821600	Enhancers	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links