Variant report

Variant	rs4648011
Chromosome Location	chr4:103475444-103475445
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	FOS	chr4:103475250-103475505	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr4:103475271-103475446	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr4:103475251-103475483	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103474531..103476175-chr4:103477255..103478902,2	MCF-7	breast:
2	chr4:103474292..103476069-chr4:103481101..103483068,2	MCF-7	breast:
3	chr4:103420331..103423503-chr4:103475320..103478755,3	MCF-7	breast:

Variant related genes	Relation type
NFKB1	TF binding region
ENSG00000109320	Chromatin interaction
ENSG00000260651	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1005819	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1020759	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs1020760	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11722146	0.91[JPT][hapmap]
rs11723120	0.90[JPT][hapmap]
rs118882	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs12509517	0.91[JPT][hapmap]
rs1585213	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs1585215	1.00[JPT][hapmap]
rs1598859	0.83[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap]
rs1599961	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs17032705	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs170731	1.00[JPT][hapmap]
rs1801	0.91[JPT][hapmap]
rs2168805	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs230491	1.00[JPT][hapmap]
rs230492	1.00[JPT][hapmap]
rs230493	0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs230495	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230496	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230498	0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs230500	0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs230504	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap]
rs230505	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs230509	1.00[JPT][hapmap]
rs230514	1.00[JPT][hapmap]
rs230515	1.00[JPT][hapmap]
rs230516	1.00[JPT][hapmap]
rs230519	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs230520	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs230521	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230525	0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs230526	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap]
rs230528	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs230529	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs230530	0.84[CHD][hapmap]
rs230531	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs230532	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs230533	1.00[JPT][hapmap]
rs230534	1.00[JPT][hapmap]
rs230535	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs230539	0.95[JPT][hapmap]
rs230540	0.91[JPT][hapmap]
rs230541	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs230542	0.83[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap]
rs3755867	0.91[JPT][hapmap]
rs3774933	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3774936	1.00[JPT][hapmap]
rs3774937	0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs3774938	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3774956	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs3774959	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs3774963	0.90[JPT][hapmap]
rs3774964	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap]
rs3817685	0.95[JPT][hapmap]
rs3821958	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4235404	1.00[JPT][hapmap]
rs4648055	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs4648058	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs4648068	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs4698858	0.85[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap]
rs4699030	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap]
rs747559	0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs93059	0.84[CHD][hapmap]
rs9790601	0.91[JPT][hapmap]
rs980455	0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]

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	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003490	chr4:103391483-103521772	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1004030	chr4:103419352-103504042	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537203	chr4:103419352-103504042	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4648011	MAPKSP1	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103440000-103484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:103440200-103478600	Weak transcription	Right Ventricle	heart
3	chr4:103440200-103488200	Weak transcription	Gastric	stomach
4	chr4:103441400-103482000	Weak transcription	Spleen	Spleen
5	chr4:103443200-103496000	Weak transcription	A549	lung
6	chr4:103445000-103496600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:103456800-103475600	Weak transcription	Brain Anterior Caudate	brain
8	chr4:103461200-103487800	Weak transcription	Colonic Mucosa	Colon
9	chr4:103461200-103490400	Weak transcription	Dnd41	blood
10	chr4:103461600-103485400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:103461600-103496400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:103463200-103481800	Weak transcription	Fetal Thymus	thymus
13	chr4:103464600-103488200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:103466600-103481200	Weak transcription	Fetal Intestine Small	intestine
15	chr4:103466800-103498600	Weak transcription	Placenta	Placenta
16	chr4:103467000-103495600	Weak transcription	HepG2	liver
17	chr4:103467200-103485400	Weak transcription	HMEC	breast
18	chr4:103468800-103490400	Weak transcription	Stomach Mucosa	stomach
19	chr4:103469600-103498000	Weak transcription	Esophagus	oesophagus
20	chr4:103469800-103481200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr4:103470000-103480800	Weak transcription	Lung	lung
22	chr4:103470000-103482600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr4:103470000-103483000	Weak transcription	Pancreas	Pancrea
24	chr4:103470000-103485400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:103470000-103485400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:103470000-103485400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr4:103470000-103498000	Weak transcription	Fetal Stomach	stomach
28	chr4:103470200-103478600	Weak transcription	Left Ventricle	heart
29	chr4:103470400-103482000	Weak transcription	Ovary	ovary
30	chr4:103470800-103484000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:103471400-103475800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr4:103472400-103475600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr4:103472600-103475600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:103472600-103480600	Weak transcription	Right Atrium	heart
35	chr4:103472800-103475800	Weak transcription	Adipose Nuclei	Adipose
36	chr4:103473000-103476200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr4:103473200-103476000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr4:103473200-103476200	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr4:103473200-103476200	Enhancers	Colon Smooth Muscle	Colon
40	chr4:103473200-103476600	Enhancers	HSMMtube	muscle
41	chr4:103473200-103478200	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr4:103473400-103481000	Weak transcription	Liver	Liver
43	chr4:103473400-103481000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr4:103473400-103481600	Weak transcription	Fetal Intestine Large	intestine
45	chr4:103473400-103482000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr4:103473400-103524600	Weak transcription	Fetal Brain Male	brain
47	chr4:103473600-103475800	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr4:103473600-103475800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr4:103473600-103476200	Enhancers	NH-A	brain
50	chr4:103473600-103481600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links