Variant report

Variant	rs10031525
Chromosome Location	chr4:54519579-54519580
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	RFX5	chr4:54519552-54519984	GM12878	blood:	n/a	n/a
2	CUX1	chr4:54519467-54520799	GM12878	blood:	n/a	chr4:54519848-54519857
3	MAFF	chr4:54519295-54519584	HepG2	liver:	n/a	n/a
4	EBF1	chr4:54519519-54521014	GM12878	blood:	n/a	n/a
5	RCOR1	chr4:54519556-54520841	GM12878	blood:	n/a	n/a
6	RUNX3	chr4:54519574-54520877	GM12878	blood:	n/a	n/a
7	RELA	chr4:54519549-54520902	GM15510	blood:	n/a	chr4:54520582-54520591 chr4:54520582-54520591

Variant related genes	Relation type
LNX1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10005578	0.92[ASN][1000 genomes]
rs10006267	0.92[ASN][1000 genomes]
rs10010205	0.92[ASN][1000 genomes]
rs10021678	0.90[ASN][1000 genomes]
rs10027185	0.97[ASN][1000 genomes]
rs10027544	0.96[ASN][1000 genomes]
rs10031866	0.91[ASN][1000 genomes]
rs1039985	0.86[ASN][1000 genomes]
rs12645402	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13146347	0.97[ASN][1000 genomes]
rs13148245	0.92[ASN][1000 genomes]
rs1477878	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1477880	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17083218	0.92[ASN][1000 genomes]
rs17083272	0.87[ASN][1000 genomes]
rs17083277	0.86[ASN][1000 genomes]
rs1991972	0.97[ASN][1000 genomes]
rs1991973	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2086048	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2219742	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3942650	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864809	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554120	0.98[ASN][1000 genomes]
rs6554121	0.97[ASN][1000 genomes]
rs6816209	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6818959	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6822736	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6843799	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6849381	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6858782	0.98[ASN][1000 genomes]
rs750695	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7688605	0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10031525	FIP1L1	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54507800-54520600	Weak transcription	Gastric	stomach
2	chr4:54511400-54520600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:54513400-54519600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:54515600-54522400	Enhancers	Stomach Mucosa	stomach
5	chr4:54515800-54520800	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr4:54515800-54521000	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr4:54516400-54520600	Weak transcription	Pancreas	Pancrea
8	chr4:54516800-54521000	Enhancers	Fetal Intestine Large	intestine
9	chr4:54517000-54520200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:54517000-54521000	Enhancers	Fetal Intestine Small	intestine
11	chr4:54517600-54523200	Weak transcription	Spleen	Spleen
12	chr4:54517800-54520400	Weak transcription	HMEC	breast
13	chr4:54517800-54520800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:54518000-54519600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:54518000-54519600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:54518000-54519600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:54518000-54519600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:54518000-54519600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:54518000-54519600	Weak transcription	HSMMtube	muscle
20	chr4:54518000-54520400	Weak transcription	NHEK	skin
21	chr4:54518000-54521200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:54518000-54523200	Weak transcription	HSMM	muscle
23	chr4:54518400-54520800	Enhancers	Fetal Kidney	kidney
24	chr4:54518600-54519600	Weak transcription	Right Ventricle	heart
25	chr4:54518600-54520800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr4:54518600-54521000	Enhancers	Duodenum Mucosa	Duodenum
27	chr4:54518800-54519600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:54518800-54519600	Weak transcription	Left Ventricle	heart
29	chr4:54518800-54519600	Weak transcription	Right Atrium	heart
30	chr4:54518800-54519800	Weak transcription	Placenta	Placenta
31	chr4:54518800-54519800	Weak transcription	Psoas Muscle	Psoas
32	chr4:54518800-54520000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr4:54518800-54520000	Enhancers	Adipose Nuclei	Adipose
34	chr4:54518800-54520800	Enhancers	Liver	Liver
35	chr4:54518800-54521000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:54518800-54521400	Weak transcription	Esophagus	oesophagus
37	chr4:54518800-54521800	Weak transcription	Small Intestine	intestine
38	chr4:54519000-54519600	Weak transcription	NHLF	lung
39	chr4:54519200-54519600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr4:54519200-54520800	Enhancers	Fetal Heart	heart
41	chr4:54519400-54519600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr4:54519400-54520200	Enhancers	Lung	lung
43	chr4:54519400-54520200	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr4:54519400-54520200	Flanking Active TSS	GM12878-XiMat	blood
45	chr4:54519400-54521600	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr4:54519400-54522000	Enhancers	Colon Smooth Muscle	Colon
47	chr4:54519400-54523600	Enhancers	Fetal Muscle Leg	muscle

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