Variant report

Variant	rs1540603
Chromosome Location	chr5:17220275-17220276
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:17217589-17221710	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:17218968-17220438	A549	lung:	n/a	n/a
3	POLR2A	chr5:17216079-17220341	Hela-S3	cervix:	n/a	n/a
4	CHD1	chr5:17218465-17220357	GM12878	blood:	n/a	chr5:17218841-17218851
5	WRNIP1	chr5:17218934-17220451	GM12878	blood:	n/a	n/a
6	REST	chr5:17215249-17221561	H1-neurons	neurons:	n/a	chr5:17217790-17217803
7	POLR2A	chr5:17217582-17221092	GM12878	blood:	n/a	n/a
8	POLR2A	chr5:17220019-17220399	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr5:17218387-17220489	GM12878	blood:	n/a	n/a
10	POLR2A	chr5:17220102-17220486	U87	brain:	n/a	n/a
11	POLR2A	chr5:17220091-17220486	U87	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:17215544..17223113-chr5:17298591..17308160,18	MCF-7	breast:
2	chr5:17219335..17222848-chr5:17226972..17230280,3	MCF-7	breast:
3	chr5:17215446..17220855-chr5:17303141..17309835,13	MCF-7	breast:
4	chr5:17218090..17220467-chr5:17258219..17260640,2	MCF-7	breast:
5	chr5:17219127..17220679-chr5:17282330..17284104,2	MCF-7	breast:
6	chr5:17218817..17220341-chr5:17246031..17248569,2	MCF-7	breast:
7	chr5:17218608..17221009-chr5:18112686..18115024,2	MCF-7	breast:
8	chr5:17220220..17221881-chr5:17313520..17315021,2	MCF-7	breast:
9	chr5:17217945..17220809-chr5:17231815..17233949,2	MCF-7	breast:
10	chr5:17219030..17221287-chr5:18110895..18114151,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000215196	TF binding region
ENSG00000185296	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs6895041	1.00[CEU][hapmap]
rs7713193	1.00[CEU][hapmap]

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	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv830218	chr5:17093162-17290045	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv4738	chr5:17178267-17223677	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv521697	chr5:17211649-17225333	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv597312	chr5:17214901-17225333	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17213600-17222200	Active TSS	Fetal Brain Female	brain
2	chr5:17215400-17221000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:17215800-17220400	Active TSS	Brain Anterior Caudate	brain
4	chr5:17216400-17221000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:17216600-17220800	Active TSS	Brain Angular Gyrus	brain
6	chr5:17218200-17221000	Active TSS	Fetal Brain Male	brain
7	chr5:17218800-17225400	Transcr. at gene 5' and 3'	A549	lung
8	chr5:17219000-17220400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:17219000-17220600	Flanking Active TSS	HUVEC	blood vessel
10	chr5:17219000-17220800	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr5:17219200-17220400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:17219200-17220400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:17219200-17220800	Transcr. at gene 5' and 3'	NHLF	lung
14	chr5:17219400-17220400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr5:17219400-17220400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr5:17219400-17220400	Active TSS	Brain Cingulate Gyrus	brain
17	chr5:17219400-17220400	Transcr. at gene 5' and 3'	NHEK	skin
18	chr5:17219400-17220600	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
19	chr5:17219400-17220600	Weak transcription	Gastric	stomach
20	chr5:17219400-17220800	Active TSS	Brain Germinal Matrix	brain
21	chr5:17219600-17220400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:17219600-17220400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
23	chr5:17219600-17220400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:17219600-17220400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr5:17219600-17220400	Enhancers	Brain Substantia Nigra	brain
26	chr5:17219600-17221000	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr5:17219600-17221000	Transcr. at gene 5' and 3'	Hela-S3	cervix
28	chr5:17219600-17222000	Enhancers	Primary B cells from peripheral blood	blood
29	chr5:17219600-17222200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:17219600-17222200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:17219600-17222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:17219600-17222400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:17219600-17223600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr5:17219600-17223800	Weak transcription	Ovary	ovary
35	chr5:17219600-17225200	Weak transcription	Fetal Stomach	stomach
36	chr5:17219800-17220800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
37	chr5:17219800-17221000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr5:17219800-17221400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:17219800-17221800	Strong transcription	HSMM	muscle
40	chr5:17219800-17222200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:17219800-17222400	Weak transcription	HSMMtube	muscle
42	chr5:17219800-17222600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr5:17219800-17223200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr5:17219800-17223200	Weak transcription	HMEC	breast
45	chr5:17219800-17223600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:17219800-17231800	Weak transcription	Fetal Kidney	kidney
47	chr5:17219800-17233600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr5:17220000-17220400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr5:17220000-17220400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:17220000-17220400	Active TSS	Primary hematopoietic stem cells	blood

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