Variant report

Variant	rs9901555
Chromosome Location	chr17:15418557-15418558
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	chr17:15411701..15413782-chr17:15416873..15418569,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11078306	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11655100	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11869273	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12325899	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12709321	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12947500	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1548681	0.88[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16951580	0.88[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2323736	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2938175	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4791624	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7209897	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215138	0.93[CHB][hapmap];0.81[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7215630	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7218204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219580	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7219850	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8071399	0.84[ASN][1000 genomes]
rs880533	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9674557	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9899976	0.85[ASN][1000 genomes]
rs9904490	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9904986	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9908576	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9915127	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	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
3	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription 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	34 gene(s)	inside rSNPs	diseases
5	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
6	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15383200-15419600	Weak transcription	Thymus	Thymus
2	chr17:15383400-15455000	Weak transcription	Gastric	stomach
3	chr17:15393400-15451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr17:15394800-15450800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr17:15396800-15420400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:15401200-15420400	Weak transcription	Psoas Muscle	Psoas
7	chr17:15405400-15419000	Weak transcription	Liver	Liver
8	chr17:15406200-15420600	Weak transcription	Colonic Mucosa	Colon
9	chr17:15406600-15419000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr17:15406600-15419800	Weak transcription	NHEK	skin
11	chr17:15406600-15422800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr17:15406600-15428800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr17:15406800-15418600	Weak transcription	Spleen	Spleen
14	chr17:15406800-15419000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr17:15406800-15419200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr17:15406800-15419400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr17:15406800-15419400	Weak transcription	Fetal Kidney	kidney
18	chr17:15406800-15419600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr17:15406800-15420200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr17:15406800-15421800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr17:15406800-15422000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr17:15406800-15450600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr17:15407000-15419000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr17:15407000-15422400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr17:15410200-15426200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr17:15410800-15418600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr17:15410800-15418600	Weak transcription	Brain Germinal Matrix	brain
28	chr17:15410800-15429000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:15413000-15419200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr17:15413200-15419400	Weak transcription	Lung	lung
31	chr17:15413200-15420000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr17:15413800-15418800	Weak transcription	Adipose Nuclei	Adipose
33	chr17:15413800-15428000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr17:15414000-15418600	Weak transcription	A549	lung
35	chr17:15414000-15429000	Weak transcription	Fetal Heart	heart
36	chr17:15414000-15430200	Weak transcription	Right Ventricle	heart
37	chr17:15414400-15418800	Enhancers	Brain Cingulate Gyrus	brain
38	chr17:15414400-15421000	Weak transcription	Left Ventricle	heart
39	chr17:15414600-15418600	Enhancers	Brain Angular Gyrus	brain
40	chr17:15414600-15422200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr17:15414600-15428000	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr17:15415200-15422400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr17:15415200-15422600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr17:15415400-15420000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr17:15415400-15422400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr17:15416200-15419000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr17:15416200-15420000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr17:15416200-15466000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr17:15416400-15420400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr17:15416400-15421800	Strong transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links