Variant report

Variant	rs3760183
Chromosome Location	chr17:17400972-17400973
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:17399723-17401178	A549	lung:	n/a	chr17:17400289-17400310 chr17:17400287-17400305 chr17:17400290-17400303 chr17:17400288-17400304 chr17:17400300-17400313
2	SMC3	chr17:17399200-17401002	SK-N-SH	brain:	n/a	chr17:17400289-17400303 chr17:17400299-17400313

No.	Distal block	Cell Line	Cell type
1	chr17:17379236..17381999-chr17:17395224..17401626,6	MCF-7	breast:
2	chr17:17396995..17404908-chr17:17406815..17414609,13	MCF-7	breast:
3	chr17:17399866..17402763-chr17:17404179..17406127,2	MCF-7	breast:
4	chr17:17380261..17384039-chr17:17397347..17401058,7	MCF-7	breast:
5	chr17:17400013..17403525-chr17:17411408..17414122,3	MCF-7	breast:
6	chr17:17398348..17401153-chr17:17494060..17496594,3	MCF-7	breast:
7	chr17:17254341..17256825-chr17:17400091..17402826,3	MCF-7	breast:

Variant related genes	Relation type
RASD1	TF binding region
ENSG00000265511	Chromatin interaction
ENSG00000141026	Chromatin interaction
ENSG00000133027	Chromatin interaction
ENSG00000264666	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1020696	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1020697	0.89[GIH][hapmap]
rs55874034	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56126242	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61398800	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	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	nsv907729	chr17:17338536-17425279	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv907730	chr17:17358004-17415217	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	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
5	nsv907732	chr17:17381764-17415217	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv907733	chr17:17381764-17422608	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv907734	chr17:17381764-17425858	Enhancers Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv907737	chr17:17388167-17411030	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3760183	SHMT1	cis	cerebellum	SCAN
rs3760183	SMCR8	cis	cerebellum	SCAN
rs3760183	TOM1L2	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17399600-17401000	Enhancers	Fetal Brain Male	brain
2	chr17:17399600-17413800	Weak transcription	Dnd41	blood
3	chr17:17399800-17401000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr17:17400200-17401000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:17400200-17401000	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr17:17400200-17401000	Bivalent Enhancer	Fetal Stomach	stomach
7	chr17:17400200-17401000	Enhancers	NHDF-Ad	bronchial
8	chr17:17400200-17401200	Enhancers	Gastric	stomach
9	chr17:17400200-17401400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr17:17400200-17402400	Enhancers	Stomach Mucosa	stomach
11	chr17:17400400-17401000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
12	chr17:17400400-17401000	Enhancers	Fetal Heart	heart
13	chr17:17400400-17401000	Flanking Active TSS	Hela-S3	cervix
14	chr17:17400600-17401000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr17:17400600-17401000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr17:17400600-17401000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr17:17400600-17401000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr17:17400600-17401000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr17:17400600-17401000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:17400600-17401000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr17:17400600-17401000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr17:17400600-17401000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr17:17400600-17401000	ZNF genes & repeats	Fetal Intestine Small	intestine
24	chr17:17400600-17401000	Enhancers	Fetal Thymus	thymus
25	chr17:17400600-17401000	Bivalent Enhancer	HMEC	breast
26	chr17:17400600-17401000	Enhancers	HUVEC	blood vessel
27	chr17:17400600-17401200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:17400600-17401200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr17:17400600-17401200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
30	chr17:17400600-17401200	Enhancers	Adipose Nuclei	Adipose
31	chr17:17400600-17401400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr17:17400600-17401600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr17:17400600-17401600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr17:17400600-17401600	Enhancers	Colonic Mucosa	Colon
35	chr17:17400600-17401600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr17:17400600-17402000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr17:17400600-17402000	Enhancers	Fetal Muscle Leg	muscle
38	chr17:17400600-17402600	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr17:17400600-17402600	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr17:17400600-17406800	Weak transcription	Brain Angular Gyrus	brain
41	chr17:17400600-17409800	Weak transcription	Esophagus	oesophagus
42	chr17:17400600-17410000	Weak transcription	Liver	Liver
43	chr17:17400600-17415200	Weak transcription	Ovary	ovary
44	chr17:17400600-17422000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:17400800-17401000	Enhancers	H1 Cell Line	embryonic stem cell
46	chr17:17400800-17401000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr17:17400800-17401000	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr17:17400800-17401000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
49	chr17:17400800-17401000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr17:17400800-17401000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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