Variant report

Variant	rs9897362
Chromosome Location	chr17:17456746-17456747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17449610..17452428-chr17:17454870..17458943,3	MCF-7	breast:
2	chr17:17451529..17456162-chr17:17456259..17460340,5	K562	blood:
3	chr17:17456555..17458234-chr17:17467873..17470234,2	MCF-7	breast:
4	chr17:17398601..17400670-chr17:17453497..17457003,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108551	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10401038	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11078396	0.85[GIH][hapmap]
rs11651280	0.90[EUR][1000 genomes]
rs11653424	0.85[GIH][hapmap]
rs11653696	1.00[GIH][hapmap]
rs11654553	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11654777	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11656769	1.00[GIH][hapmap]
rs11658311	1.00[CEU][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11658944	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs11659047	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs13342397	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16961845	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28583584	0.89[EUR][1000 genomes]
rs28636952	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28652618	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35301480	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35838363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56030759	0.87[EUR][1000 genomes]
rs58729290	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60831194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7210978	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7214152	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7214988	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7215055	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7216223	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7217764	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap]
rs7219568	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs7222358	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7224725	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7225421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73978969	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8064558	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8070432	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8074742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8078513	1.00[CEU][hapmap]
rs8081961	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs897456	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs9889584	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9889795	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9890062	0.82[AMR][1000 genomes]
rs9896285	1.00[CEU][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap]
rs9903468	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9903503	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9904004	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9905032	1.00[CEU][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9905191	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9910075	0.85[GIH][hapmap]
rs9910151	1.00[CEU][hapmap]
rs9910747	1.00[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9911823	1.00[CEU][hapmap]
rs9944423	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907731	chr17:17358004-17504856	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv907736	chr17:17381764-17465458	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv907744	chr17:17404586-17504856	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv907746	chr17:17412032-17478917	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv907747	chr17:17412032-17504856	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
7	nsv470579	chr17:17424332-17493810	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
9	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv907750	chr17:17439458-17460180	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 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	chr17:17418200-17478000	Weak transcription	Primary T cells from cord blood	blood
2	chr17:17424600-17460000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr17:17436800-17479200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr17:17443400-17467000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr17:17444200-17467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:17444400-17469200	Weak transcription	Fetal Brain Female	brain
7	chr17:17444600-17460400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr17:17444600-17464600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr17:17444800-17464000	Weak transcription	Esophagus	oesophagus
10	chr17:17445200-17468400	Weak transcription	Thymus	Thymus
11	chr17:17445200-17473200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr17:17447400-17461000	Weak transcription	Pancreas	Pancrea
13	chr17:17449000-17459000	Weak transcription	Spleen	Spleen
14	chr17:17449000-17464800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr17:17449600-17464800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:17449600-17467000	Weak transcription	Ovary	ovary
17	chr17:17450800-17467800	Weak transcription	Brain Germinal Matrix	brain
18	chr17:17451000-17468400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr17:17451400-17461200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr17:17453200-17457400	Enhancers	Left Ventricle	heart
21	chr17:17453200-17468200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr17:17453400-17477800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr17:17453600-17457000	Enhancers	Right Ventricle	heart
24	chr17:17454800-17459000	Enhancers	Fetal Muscle Trunk	muscle
25	chr17:17454800-17469800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr17:17455000-17457400	Enhancers	Psoas Muscle	Psoas
27	chr17:17455000-17460000	Weak transcription	Brain Hippocampus Middle	brain
28	chr17:17455000-17462600	Weak transcription	Gastric	stomach
29	chr17:17455000-17468600	Weak transcription	Brain Substantia Nigra	brain
30	chr17:17455200-17457600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr17:17455200-17459000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr17:17455200-17459200	Weak transcription	Lung	lung
33	chr17:17455200-17460200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr17:17455200-17463200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr17:17455200-17466400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr17:17455200-17466800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr17:17455200-17468000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr17:17455200-17468000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr17:17455200-17469200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr17:17455200-17471800	Weak transcription	HepG2	liver
41	chr17:17455400-17457800	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr17:17455600-17457800	Enhancers	Right Atrium	heart
43	chr17:17455800-17456800	Strong transcription	Fetal Intestine Small	intestine
44	chr17:17455800-17456800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr17:17456000-17456800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr17:17456000-17461000	Weak transcription	Liver	Liver
47	chr17:17456200-17456800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr17:17456200-17468000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr17:17456400-17458000	Enhancers	Fetal Heart	heart
50	chr17:17456400-17458000	Strong transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links