Variant report

Variant	rs4646385
Chromosome Location	chr17:17448691-17448692
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17432762..17434995-chr17:17447449..17449700,2	K562	blood:
2	chr17:17447568..17449636-chr17:17462055..17463779,2	MCF-7	breast:
3	chr17:17447456..17449744-chr17:17453079..17454836,2	K562	blood:
4	chr17:17434263..17436931-chr17:17447202..17448742,2	K562	blood:
5	chr17:17439547..17441948-chr17:17448069..17450989,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RASD1-2	chr17:17447584-17449725	NONHSAT146094

No data

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11078389	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11651620	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11656215	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11867345	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11871667	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12939945	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12941371	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12945144	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1531100	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35656361	0.81[AMR][1000 genomes]
rs4244593	0.84[CEU][hapmap]
rs4646346	0.96[ASN][1000 genomes]
rs4646349	0.96[ASN][1000 genomes]
rs4646352	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4646356	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4646358	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4646359	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4646365	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646368	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4646369	0.96[ASN][1000 genomes]
rs4646387	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4646388	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646389	0.92[CEU][hapmap]
rs4646390	0.86[CEU][hapmap]
rs4646391	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4646392	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4646394	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4646395	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4646396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646402	0.84[CEU][hapmap]
rs4646405	0.88[CEU][hapmap]
rs4924922	0.81[CEU][hapmap]
rs6502603	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs729975	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs744925	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs746899	0.84[CEU][hapmap]
rs747770	0.88[CEU][hapmap]
rs748196	0.88[CEU][hapmap]
rs750546	0.85[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs897450	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs936108	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9893179	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9894588	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4646385	CDRT1	cis	parietal	SCAN
rs4646385	COPS3	cis	cerebellum	SCAN
rs4646385	SNORD49B	cis	parietal	SCAN

Chromatin state (count:64 , 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	chr17:17438800-17450800	Enhancers	Fetal Muscle Leg	muscle
5	chr17:17439800-17453200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr17:17440000-17453200	Weak transcription	Brain Substantia Nigra	brain
7	chr17:17440200-17454800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr17:17440400-17450000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr17:17442800-17456400	Weak transcription	Small Intestine	intestine
10	chr17:17443400-17467000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr17:17444000-17454400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr17:17444000-17454400	Weak transcription	Placenta	Placenta
13	chr17:17444200-17451600	Weak transcription	Lung	lung
14	chr17:17444200-17454400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr17:17444200-17467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:17444400-17449800	Weak transcription	HepG2	liver
17	chr17:17444400-17469200	Weak transcription	Fetal Brain Female	brain
18	chr17:17444600-17449400	Weak transcription	Brain Hippocampus Middle	brain
19	chr17:17444600-17449600	Weak transcription	Fetal Intestine Large	intestine
20	chr17:17444600-17449600	Weak transcription	Left Ventricle	heart
21	chr17:17444600-17449800	Weak transcription	Fetal Brain Male	brain
22	chr17:17444600-17450600	Weak transcription	Stomach Mucosa	stomach
23	chr17:17444600-17460400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr17:17444600-17464600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr17:17444800-17449000	Weak transcription	Fetal Heart	heart
26	chr17:17444800-17464000	Weak transcription	Esophagus	oesophagus
27	chr17:17445200-17468400	Weak transcription	Thymus	Thymus
28	chr17:17445200-17473200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr17:17446600-17449000	Enhancers	Liver	Liver
30	chr17:17446600-17451600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:17447400-17461000	Weak transcription	Pancreas	Pancrea
32	chr17:17448000-17449200	Strong transcription	Fetal Intestine Small	intestine
33	chr17:17448200-17448800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr17:17448400-17448800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:17448400-17449000	Genic enhancers	Spleen	Spleen
36	chr17:17448400-17449200	Enhancers	NHDF-Ad	bronchial
37	chr17:17448400-17449600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr17:17448400-17449600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr17:17448400-17449600	Enhancers	Adipose Nuclei	Adipose
40	chr17:17448400-17449800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr17:17448400-17449800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr17:17448400-17449800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr17:17448400-17451400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr17:17448600-17448800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr17:17448600-17448800	Weak transcription	Fetal Stomach	stomach
46	chr17:17448600-17448800	Enhancers	Right Atrium	heart
47	chr17:17448600-17448800	Enhancers	Right Ventricle	heart
48	chr17:17448600-17449000	Enhancers	Placenta Amnion	Placenta Amnion
49	chr17:17448600-17449200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr17:17448600-17449200	Enhancers	Brain Inferior Temporal Lobe	brain

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