Variant report

Variant	rs4646391
Chromosome Location	chr17:17441369-17441370
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17398006..17400229-chr17:17440042..17442151,2	MCF-7	breast:
2	chr17:17440432..17443332-chr17:17443891..17446677,2	MCF-7	breast:
3	chr17:17420339..17423033-chr17:17440049..17441973,2	MCF-7	breast:
4	chr17:17439547..17441948-chr17:17448069..17450989,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108551	Chromatin interaction
ENSG00000133027	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11078389	0.81[CEU][hapmap]
rs11651620	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654842	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11656215	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11867345	0.84[EUR][1000 genomes]
rs11871667	0.83[EUR][1000 genomes]
rs12939945	0.84[EUR][1000 genomes]
rs12941371	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12945144	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12948060	0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs1531100	0.86[EUR][1000 genomes]
rs2124344	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs35656361	0.81[AMR][1000 genomes]
rs4244593	0.92[CEU][hapmap]
rs4244596	0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4244598	0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4646350	0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4646351	0.89[ASN][1000 genomes]
rs4646352	0.86[EUR][1000 genomes]
rs4646356	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs4646357	0.89[ASN][1000 genomes]
rs4646358	0.86[EUR][1000 genomes]
rs4646359	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs4646365	0.86[EUR][1000 genomes]
rs4646368	0.86[EUR][1000 genomes]
rs4646370	0.89[ASN][1000 genomes]
rs4646372	0.89[ASN][1000 genomes]
rs4646385	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4646387	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646388	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4646389	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4646390	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4646392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646394	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646396	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4646397	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs4646402	0.92[CEU][hapmap]
rs4646405	0.81[CEU][hapmap]
rs4924922	0.88[CEU][hapmap]
rs6502603	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7209113	0.89[ASN][1000 genomes]
rs7221487	0.89[ASN][1000 genomes]
rs729974	0.89[ASN][1000 genomes]
rs744925	0.86[EUR][1000 genomes]
rs746899	0.92[CEU][hapmap]
rs747770	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs748196	0.92[CEU][hapmap]
rs750546	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8079427	0.89[ASN][1000 genomes]
rs8080165	0.98[ASN][1000 genomes]
rs8082417	0.84[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs897450	0.84[EUR][1000 genomes]
rs897451	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs936108	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9892560	0.98[ASN][1000 genomes]
rs9893179	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9894321	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482648	chr17:17315268-17455442	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	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
3	nsv907735	chr17:17381764-17448589	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	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
5	nsv907743	chr17:17404586-17448589	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	nsv907749	chr17:17417169-17448589	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv574526	chr17:17422608-17444369	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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:63 , 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	chr17:17419600-17447000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr17:17424600-17460000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr17:17432800-17442600	Weak transcription	Spleen	Spleen
5	chr17:17434800-17448600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr17:17436600-17441600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr17:17436800-17479200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr17:17438600-17442800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr17:17438600-17444800	Enhancers	Fetal Heart	heart
10	chr17:17438800-17442000	Enhancers	A549	lung
11	chr17:17438800-17445200	Enhancers	Liver	Liver
12	chr17:17438800-17450800	Enhancers	Fetal Muscle Leg	muscle
13	chr17:17439200-17441600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr17:17439200-17441600	Enhancers	Gastric	stomach
15	chr17:17439200-17441600	Enhancers	Left Ventricle	heart
16	chr17:17439200-17441600	Enhancers	Right Atrium	heart
17	chr17:17439200-17441600	Enhancers	Right Ventricle	heart
18	chr17:17439200-17444400	Enhancers	Pancreas	Pancrea
19	chr17:17439200-17444400	Enhancers	HepG2	liver
20	chr17:17439200-17444600	Enhancers	Stomach Mucosa	stomach
21	chr17:17439200-17446000	Enhancers	Fetal Muscle Trunk	muscle
22	chr17:17439400-17442400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr17:17439400-17444200	Enhancers	Duodenum Mucosa	Duodenum
24	chr17:17439600-17441600	Enhancers	Colonic Mucosa	Colon
25	chr17:17439600-17442600	Weak transcription	Fetal Lung	lung
26	chr17:17439600-17442600	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr17:17439600-17444400	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr17:17439600-17444600	Genic enhancers	Fetal Intestine Small	intestine
29	chr17:17439800-17444000	Weak transcription	Brain Anterior Caudate	brain
30	chr17:17439800-17444000	Weak transcription	Brain Hippocampus Middle	brain
31	chr17:17439800-17447000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr17:17439800-17448400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr17:17439800-17448600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr17:17439800-17448600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr17:17439800-17453200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr17:17440000-17442000	Weak transcription	Colon Smooth Muscle	Colon
37	chr17:17440000-17442600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr17:17440000-17444000	Weak transcription	Adipose Nuclei	Adipose
39	chr17:17440000-17444000	Weak transcription	Fetal Brain Female	brain
40	chr17:17440000-17444600	Enhancers	Fetal Intestine Large	intestine
41	chr17:17440000-17444600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr17:17440000-17448600	Weak transcription	HSMMtube	muscle
43	chr17:17440000-17453200	Weak transcription	Brain Substantia Nigra	brain
44	chr17:17440200-17442600	Weak transcription	Fetal Stomach	stomach
45	chr17:17440200-17443800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr17:17440200-17448400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr17:17440200-17454800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr17:17440400-17442400	Weak transcription	Lung	lung
49	chr17:17440400-17450000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr17:17440600-17441400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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