Variant report

Variant	rs17006888
Chromosome Location	chr4:84503375-84503376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:84498347..84499871-chr4:84502515..84505329,2	K562	blood:
2	chr4:84503094..84504001-chr4:84560450..84561698,5	MCF-7	breast:
3	chr4:84498263..84499871-chr4:84502131..84504015,2	K562	blood:
4	chr4:84411906..84412619-chr4:84503063..84503954,2	MCF-7	breast:
5	chr4:84429927..84430625-chr4:84503101..84503795,5	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10002139	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10009351	0.92[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.81[TSI][hapmap]
rs10012782	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11099607	0.80[ASN][1000 genomes]
rs1123378	0.80[ASN][1000 genomes]
rs11721920	0.84[ASN][1000 genomes]
rs11722160	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11723311	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11730975	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11731267	0.82[ASN][1000 genomes]
rs11731336	0.82[ASN][1000 genomes]
rs11733281	0.84[ASN][1000 genomes]
rs11733610	0.80[ASN][1000 genomes]
rs11734158	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11736724	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11737424	0.84[ASN][1000 genomes]
rs12331130	0.84[ASN][1000 genomes]
rs12331142	0.84[ASN][1000 genomes]
rs12331198	0.84[ASN][1000 genomes]
rs12331205	0.84[ASN][1000 genomes]
rs12331922	0.84[ASN][1000 genomes]
rs1521532	0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs17353060	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17355300	1.00[ASW][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17355321	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17355349	0.80[ASN][1000 genomes]
rs17355391	0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs17355663	0.95[CHB][hapmap];0.92[JPT][hapmap]
rs1965464	0.83[ASN][1000 genomes]
rs28463240	0.84[ASN][1000 genomes]
rs28482178	0.84[ASN][1000 genomes]
rs28504032	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28542730	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28587748	0.84[ASN][1000 genomes]
rs28615868	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28710332	0.84[ASN][1000 genomes]
rs35434386	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3733327	0.81[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs3733329	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs4693092	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4693093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693633	0.80[ASN][1000 genomes]
rs55724846	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55839835	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55851819	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56003368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56191639	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56208893	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56394927	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62303966	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62303968	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62303974	0.80[ASN][1000 genomes]
rs62303975	0.80[ASN][1000 genomes]
rs62305330	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62305331	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62305332	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62305333	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62305334	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62305335	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62305336	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62305339	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62305340	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62305342	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62305343	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6812240	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6812267	0.84[ASN][1000 genomes]
rs6835060	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6835481	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72654969	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72654977	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72654978	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72654987	0.80[ASN][1000 genomes]
rs9307826	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829994	chr4:84366299-84558316	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv879512	chr4:84374692-85090749	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	29 gene(s)	inside rSNPs	diseases
3	nsv1010009	chr4:84469896-84882528	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17006888	IBSP	cis	parietal	SCAN
rs17006888	AGPAT9	cis	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:84482800-84503400	Weak transcription	Ovary	ovary
2	chr4:84486000-84513000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:84488600-84516800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:84489400-84503400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr4:84492000-84512200	Weak transcription	NHEK	skin
6	chr4:84495600-84503400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:84495600-84516600	Weak transcription	Fetal Intestine Large	intestine
8	chr4:84495600-84516800	Weak transcription	Right Ventricle	heart
9	chr4:84498200-84503400	Weak transcription	Right Atrium	heart
10	chr4:84500000-84503400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:84500000-84503400	Weak transcription	Fetal Lung	lung
12	chr4:84500000-84512800	Weak transcription	Fetal Intestine Small	intestine
13	chr4:84502000-84503400	Weak transcription	Esophagus	oesophagus
14	chr4:84502200-84503400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:84502400-84504200	Enhancers	Primary B cells from peripheral blood	blood
16	chr4:84502400-84504200	Genic enhancers	A549	lung
17	chr4:84502600-84503600	Enhancers	Duodenum Mucosa	Duodenum
18	chr4:84502600-84503600	Genic enhancers	Psoas Muscle	Psoas
19	chr4:84502600-84503800	Flanking Active TSS	GM12878-XiMat	blood
20	chr4:84502600-84504000	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr4:84502600-84504000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
22	chr4:84502600-84504200	Enhancers	Primary B cells from cord blood	blood
23	chr4:84502600-84504200	Enhancers	Fetal Heart	heart
24	chr4:84502600-84504200	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr4:84502600-84504400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr4:84502800-84503600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:84502800-84503600	Weak transcription	NH-A	brain
28	chr4:84502800-84503800	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr4:84502800-84503800	Enhancers	Adipose Nuclei	Adipose
30	chr4:84502800-84503800	Genic enhancers	Left Ventricle	heart
31	chr4:84502800-84503800	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr4:84502800-84503800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
33	chr4:84502800-84504200	Enhancers	Brain Hippocampus Middle	brain
34	chr4:84503000-84503600	Enhancers	Primary hematopoietic stem cells	blood
35	chr4:84503000-84503600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr4:84503000-84504400	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr4:84503200-84504000	Enhancers	Colon Smooth Muscle	Colon
38	chr4:84503200-84504200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:84503200-84504200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr4:84503200-84504200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:84503200-84504200	Enhancers	Liver	Liver
42	chr4:84503200-84504200	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links