Variant report

Variant	rs9897551
Chromosome Location	chr17:66817866-66817867
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:66808054..66811042-chr17:66815866..66818225,2	MCF-7	breast:
2	chr17:66808533..66810777-chr17:66816260..66818804,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12451146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443264	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2009065	0.90[ASN][1000 genomes]
rs2016785	0.81[ASN][1000 genomes]
rs3826429	0.89[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4148010	0.91[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs4968823	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968961	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6501834	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs7207042	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7216979	0.86[ASN][1000 genomes]
rs7218376	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7218530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8071901	0.89[ASN][1000 genomes]
rs9893385	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9895870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9896139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9898982	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9914229	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9914659	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	16 gene(s)	inside rSNPs	diseases
3	nsv575927	chr17:66787428-66817866	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv908694	chr17:66802992-66913936	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9897551	ACE	cis	cerebellum	SCAN
rs9897551	CACNG1	cis	cerebellum	SCAN
rs9897551	ICAM2	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66814800-66818600	Enhancers	Liver	Liver
2	chr17:66815800-66818000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr17:66816000-66818600	Enhancers	Brain Hippocampus Middle	brain
4	chr17:66816600-66818400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr17:66816600-66818400	Enhancers	Brain Substantia Nigra	brain
6	chr17:66816600-66818400	Enhancers	Placenta	Placenta
7	chr17:66816600-66819200	Enhancers	NHLF	lung
8	chr17:66816800-66819400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:66816800-66819400	Enhancers	NH-A	brain
10	chr17:66817000-66818200	Enhancers	Fetal Intestine Small	intestine
11	chr17:66817000-66818800	Enhancers	Brain Cingulate Gyrus	brain
12	chr17:66817000-66818800	Enhancers	HSMMtube	muscle
13	chr17:66817000-66819000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr17:66817000-66819000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr17:66817000-66819000	Enhancers	Hela-S3	cervix
16	chr17:66817000-66819200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:66817000-66819200	Enhancers	HMEC	breast
18	chr17:66817000-66819400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr17:66817000-66819400	Enhancers	HUVEC	blood vessel
20	chr17:66817000-66819800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr17:66817000-66819800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr17:66817200-66818000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr17:66817200-66818200	Enhancers	Ovary	ovary
24	chr17:66817200-66818600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr17:66817200-66818800	Enhancers	HSMM	muscle
26	chr17:66817200-66819000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr17:66817200-66819200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr17:66817200-66819200	Enhancers	NHDF-Ad	bronchial
29	chr17:66817200-66819400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr17:66817200-66819800	Enhancers	Fetal Muscle Leg	muscle
31	chr17:66817400-66818400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr17:66817400-66818600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr17:66817400-66818800	Enhancers	Fetal Heart	heart
34	chr17:66817400-66818800	Enhancers	Osteobl	bone
35	chr17:66817600-66818400	Enhancers	Fetal Intestine Large	intestine
36	chr17:66817600-66818600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr17:66817600-66818600	Enhancers	Fetal Lung	lung
38	chr17:66817600-66818600	Weak transcription	Psoas Muscle	Psoas
39	chr17:66817600-66818600	Flanking Active TSS	HepG2	liver
40	chr17:66817600-66818800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr17:66817600-66819000	Enhancers	NHEK	skin
42	chr17:66817600-66828800	Weak transcription	Right Atrium	heart
43	chr17:66817800-66818000	Enhancers	Brain Anterior Caudate	brain
44	chr17:66817800-66818200	Flanking Active TSS	A549	lung
45	chr17:66817800-66818600	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr17:66817800-66818600	Enhancers	Adipose Nuclei	Adipose
47	chr17:66817800-66819000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links