Variant report

Variant	rs757411
Chromosome Location	chr17:38775150-38775151
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38772991..38776371-chr17:38950027..38953549,4	MCF-7	breast:
2	chr17:38711199..38713464-chr17:38773822..38775935,2	MCF-7	breast:
3	chr17:38773571..38776015-chr17:38974880..38976971,2	MCF-7	breast:
4	chr17:38771673..38774769-chr17:38774806..38776457,3	K562	blood:
5	chr17:38773127..38778716-chr17:38801405..38806004,8	MCF-7	breast:
6	chr17:38722952..38724580-chr17:38773813..38776403,2	MCF-7	breast:
7	chr17:38773408..38778160-chr17:38801455..38807561,11	MCF-7	breast:
8	chr17:38774901..38776948-chr17:38802211..38805004,2	K562	blood:
9	chr17:38732692..38734383-chr17:38772868..38775729,2	MCF-7	breast:
10	chr17:38765688..38767595-chr17:38773292..38775210,2	K562	blood:
11	chr17:38774850..38777114-chr17:38779652..38781340,2	MCF-7	breast:
12	chr17:38707503..38711120-chr17:38769935..38775644,8	MCF-7	breast:
13	chr17:38772124..38774636-chr17:38774789..38776541,3	MCF-7	breast:
14	chr17:38705642..38709928-chr17:38772338..38775854,5	MCF-7	breast:
15	chr17:38602265..38605118-chr17:38774156..38776452,3	MCF-7	breast:
16	chr17:38775118..38777132-chr17:38858165..38860352,2	MCF-7	breast:
17	chr17:38733163..38735894-chr17:38771819..38775610,4	MCF-7	breast:
18	chr17:38470862..38473621-chr17:38773618..38775413,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000073584	Chromatin interaction
ENSG00000167916	Chromatin interaction
ENSG00000167920	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1013971	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1048572	0.94[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1048573	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11658582	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014704	0.90[GIH][hapmap];0.89[JPT][hapmap]
rs2429549	0.88[GIH][hapmap]
rs3752026	0.89[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4890093	0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.94[ASN][1000 genomes]
rs4890117	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6503549	0.82[JPT][hapmap]
rs7209467	0.88[JPT][hapmap]
rs7209735	0.90[GIH][hapmap];0.87[JPT][hapmap]
rs7221109	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223136	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7223332	0.90[GIH][hapmap];0.82[JPT][hapmap]
rs7226035	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8068721	0.85[GIH][hapmap];0.83[JPT][hapmap]
rs8076587	0.83[JPT][hapmap]
rs917593	0.90[GIH][hapmap];0.83[JPT][hapmap]
rs917595	0.83[JPT][hapmap]
rs9896791	0.82[JPT][hapmap]
rs9906785	0.94[ASN][1000 genomes]
rs9911533	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915135	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv574994	chr17:38719799-38824636	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv2758454	chr17:38748300-38850104	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2758689	chr17:38748300-38850104	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS 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 miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS 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	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs757411	KLHL10	cis	cerebellum	SCAN
rs757411	SMARCE1	cis	multi-tissue	Pritchard
rs757411	TBCA	trans	cerebellum	SCAN
rs757411	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs757411	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs757411	KRT222	cis	parietal	SCAN
rs757411	TADA2A	cis	cerebellum	SCAN
rs757411	C17orf66	cis	parietal	SCAN
rs757411	WIPF2	cis	parietal	SCAN
rs757411	FLJ43826	cis	parietal	SCAN
rs757411	KRT222	cis	cerebellum	SCAN
rs757411	HNF1B	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38763400-38775600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr17:38769600-38784200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:38770800-38776200	Enhancers	Placenta	Placenta
4	chr17:38771000-38775200	Weak transcription	Fetal Kidney	kidney
5	chr17:38771400-38775200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr17:38772000-38776400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr17:38772000-38784600	Weak transcription	Gastric	stomach
8	chr17:38772000-38785000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr17:38772200-38775800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:38772200-38776200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:38772400-38775400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr17:38772400-38775400	Weak transcription	A549	lung
13	chr17:38772400-38776200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr17:38772400-38778800	Weak transcription	Spleen	Spleen
15	chr17:38772400-38783600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr17:38772600-38775400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr17:38772600-38775600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr17:38772600-38775800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr17:38772600-38785000	Weak transcription	Ovary	ovary
20	chr17:38772800-38775400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr17:38772800-38775400	Weak transcription	Fetal Thymus	thymus
22	chr17:38772800-38776000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr17:38773000-38784400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr17:38773000-38786800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr17:38773200-38775800	Weak transcription	Primary T cells from cord blood	blood
26	chr17:38773400-38775600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:38773600-38775400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr17:38773600-38775600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr17:38773600-38776000	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr17:38773800-38775200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:38773800-38775800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr17:38773800-38776600	Enhancers	Fetal Intestine Small	intestine
33	chr17:38774000-38775400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr17:38774000-38775400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr17:38774000-38775400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr17:38774200-38775200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr17:38774200-38775400	Weak transcription	Primary B cells from cord blood	blood
38	chr17:38774200-38775400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr17:38774200-38775400	Weak transcription	Colonic Mucosa	Colon
40	chr17:38774200-38776200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr17:38774200-38776600	Enhancers	Fetal Intestine Large	intestine
42	chr17:38774200-38784600	Weak transcription	Esophagus	oesophagus
43	chr17:38774400-38775400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr17:38774400-38776200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr17:38774400-38785000	Weak transcription	Lung	lung
46	chr17:38774400-38786200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr17:38774400-38789200	Weak transcription	Right Atrium	heart
48	chr17:38774600-38775800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr17:38774800-38775200	Weak transcription	Fetal Stomach	stomach
50	chr17:38775000-38776000	Flanking Active TSS	HepG2	liver

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