Variant report

Variant	rs11659024
Chromosome Location	chr17:38775805-38775806
allele	A/G
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 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	chr17:38732131..38732809-chr17:38775272..38776029,4	MCF-7	breast:
6	chr17:38773127..38778716-chr17:38801405..38806004,8	MCF-7	breast:
7	chr17:38722952..38724580-chr17:38773813..38776403,2	MCF-7	breast:
8	chr17:38773408..38778160-chr17:38801455..38807561,11	MCF-7	breast:
9	chr17:38774901..38776948-chr17:38802211..38805004,2	K562	blood:
10	chr17:38775796..38779705-chr17:38780974..38783224,4	MCF-7	breast:
11	chr17:38774850..38777114-chr17:38779652..38781340,2	MCF-7	breast:
12	chr17:38772124..38774636-chr17:38774789..38776541,3	MCF-7	breast:
13	chr17:38775410..38776798-chr17:38947797..38948579,4	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:

No data

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

Extended variants
information (count: 35 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11654834	0.87[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1474454	0.81[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs16966093	0.87[ASN][1000 genomes]
rs2429548	0.81[ASW][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.89[YRI][hapmap]
rs2429551	0.83[JPT][hapmap]
rs2429552	0.95[CHD][hapmap];0.80[GIH][hapmap];0.82[MEX][hapmap]
rs2462957	0.82[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap]
rs2462960	0.82[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.93[YRI][hapmap]
rs2462961	0.95[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap]
rs2462966	0.95[CHD][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap]
rs2469817	0.95[CHD][hapmap];0.80[GIH][hapmap];0.82[MEX][hapmap]
rs2469820	0.95[CHD][hapmap];0.80[GIH][hapmap];0.82[MEX][hapmap]
rs2469825	0.82[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap]
rs55664118	0.93[ASN][1000 genomes]
rs6503545	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6503546	0.87[ASN][1000 genomes]
rs67138687	0.87[ASN][1000 genomes]
rs7218478	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7224919	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs723728	0.82[GIH][hapmap]
rs723729	0.90[CHD][hapmap]
rs8066541	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8074179	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8074758	0.81[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap]
rs874889	0.82[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs887376	0.82[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs9303294	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9630727	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9630729	0.88[ASN][1000 genomes]
rs9894823	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9902509	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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
rs11659024	KRT24	cis	Esophagus Mucosa	GTEx
rs11659024	TADA2A	cis	cerebellum	SCAN
rs11659024	SMARCE1	cis	multi-tissue	Pritchard
rs11659024	KLHL10	cis	cerebellum	SCAN
rs11659024	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs11659024	TBCA	trans	cerebellum	SCAN
rs11659024	CCL4	cis	parietal	SCAN
rs11659024	PEX12	cis	parietal	SCAN
rs11659024	HNF1B	cis	cerebellum	SCAN
rs11659024	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs11659024	KRT222	cis	cerebellum	SCAN
rs11659024	FLJ43826	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38769600-38784200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr17:38770800-38776200	Enhancers	Placenta	Placenta
3	chr17:38772000-38776400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr17:38772000-38784600	Weak transcription	Gastric	stomach
5	chr17:38772000-38785000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr17:38772200-38776200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr17:38772400-38776200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr17:38772400-38778800	Weak transcription	Spleen	Spleen
9	chr17:38772400-38783600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr17:38772600-38785000	Weak transcription	Ovary	ovary
11	chr17:38772800-38776000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr17:38773000-38784400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr17:38773000-38786800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr17:38773600-38776000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr17:38773800-38776600	Enhancers	Fetal Intestine Small	intestine
16	chr17:38774200-38776200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr17:38774200-38776600	Enhancers	Fetal Intestine Large	intestine
18	chr17:38774200-38784600	Weak transcription	Esophagus	oesophagus
19	chr17:38774400-38776200	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr17:38774400-38785000	Weak transcription	Lung	lung
21	chr17:38774400-38786200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr17:38774400-38789200	Weak transcription	Right Atrium	heart
23	chr17:38775000-38776000	Flanking Active TSS	HepG2	liver
24	chr17:38775000-38776400	Enhancers	Liver	Liver
25	chr17:38775200-38776000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr17:38775200-38776800	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr17:38775200-38779000	Enhancers	Fetal Stomach	stomach
28	chr17:38775400-38776000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr17:38775400-38776000	Enhancers	Colonic Mucosa	Colon
30	chr17:38775400-38776200	Enhancers	Primary B cells from cord blood	blood
31	chr17:38775400-38776200	Enhancers	Primary B cells from peripheral blood	blood
32	chr17:38775400-38776200	Enhancers	Primary T cells fromperipheralblood	blood
33	chr17:38775400-38776200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr17:38775400-38776200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr17:38775400-38776200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr17:38775400-38776200	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr17:38775400-38776200	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr17:38775400-38776200	Enhancers	Duodenum Mucosa	Duodenum
39	chr17:38775400-38776200	Enhancers	A549	lung
40	chr17:38775400-38776400	Weak transcription	Fetal Kidney	kidney
41	chr17:38775400-38779000	Enhancers	Fetal Thymus	thymus
42	chr17:38775600-38776200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr17:38775600-38776200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr17:38775600-38776200	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr17:38775600-38784600	Weak transcription	Pancreas	Pancrea
46	chr17:38775800-38776200	Enhancers	Primary T cells from cord blood	blood
47	chr17:38775800-38776200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr17:38775800-38776400	Enhancers	Fetal Muscle Leg	muscle
49	chr17:38775800-38776600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr17:38775800-38776600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links