Variant report

Variant	rs7705279
Chromosome Location	chr5:95324375-95324376
allele	A/G
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	FOXA1	chr5:95323671-95325502	HepG2	liver:	n/a	chr5:95324610-95324622 chr5:95324819-95324831 chr5:95324931-95324943
2	NFIC	chr5:95323477-95325436	HepG2	liver:	n/a	n/a
3	FOXA2	chr5:95322332-95325466	HepG2	liver:	n/a	chr5:95324610-95324622 chr5:95324819-95324831 chr5:95324931-95324943
4	ARID3A	chr5:95323723-95325371	HepG2	liver:	n/a	n/a
5	MAX	chr5:95323689-95325301	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:95322628..95324639-chr5:95325581..95328091,2	K562	blood:
2	chr5:95315592..95318103-chr5:95322606..95324931,2	K562	blood:
3	chr5:95322876..95325746-chr5:95335508..95338099,2	K562	blood:

Variant related genes	Relation type
ENSG00000250955	TF binding region

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10052503	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10069748	0.87[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs10073752	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[EUR][1000 genomes]
rs10515232	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1057963	0.86[CHB][hapmap]
rs1057964	0.87[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs11741590	0.87[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs11744881	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs12055262	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1423268	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs1423269	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs1458017	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs1458018	0.87[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs17085249	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs17085333	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1841010	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs1862313	0.92[EUR][1000 genomes]
rs2042340	0.86[CHB][hapmap]
rs2112566	0.95[EUR][1000 genomes]
rs2161318	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2270554	0.87[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs2348984	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2546199	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2548594	0.87[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs3734131	0.95[EUR][1000 genomes]
rs3756703	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3777162	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3777163	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3777164	0.81[EUR][1000 genomes]
rs3777165	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs3777166	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[EUR][1000 genomes]
rs3777167	0.84[CEU][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs3777168	0.95[EUR][1000 genomes]
rs3777171	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs3777173	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs3777175	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs3777178	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777179	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs3777184	0.86[CHB][hapmap]
rs3777185	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs3777188	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs3777189	0.86[CHB][hapmap]
rs3777190	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs3777193	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs3777194	0.87[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs3777196	0.87[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs3777200	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs3777204	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs3777207	0.86[TSI][hapmap]
rs3815768	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs3822750	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4642392	0.87[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap]
rs55841351	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56002885	0.92[EUR][1000 genomes]
rs57243277	0.95[EUR][1000 genomes]
rs57595413	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58921760	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59307279	0.91[EUR][1000 genomes]
rs6556894	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6861531	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6877821	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6881355	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6881872	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6883880	0.92[EUR][1000 genomes]
rs6885567	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs6889029	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs6894651	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6897997	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6898371	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6898399	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72656689	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7700895	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7705720	0.95[EUR][1000 genomes]
rs7710422	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7724599	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs889302	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs918629	0.86[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs9314162	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv823146	chr5:95300912-95453557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	esv2757121	chr5:95304236-95539536	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	esv34203	chr5:95310985-95452324	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7705279	ELL2	Cis_1M	lymphoblastoid	RTeQTL
rs7705279	ERAP1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95318200-95325000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:95318200-95327600	Enhancers	Fetal Intestine Small	intestine
3	chr5:95319600-95325600	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr5:95320000-95327600	Enhancers	Fetal Intestine Large	intestine
5	chr5:95320600-95324800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr5:95320600-95330800	Weak transcription	HSMM	muscle
7	chr5:95321800-95325000	Weak transcription	Aorta	Aorta
8	chr5:95321800-95325200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:95322200-95324800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:95322200-95324800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:95322800-95330800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:95322800-95331800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:95323000-95324600	Flanking Active TSS	Liver	Liver
14	chr5:95323200-95324600	Weak transcription	Fetal Heart	heart
15	chr5:95323200-95325000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:95323200-95333000	Weak transcription	Stomach Mucosa	stomach
17	chr5:95323600-95325600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:95323800-95324400	Enhancers	HepG2	liver
19	chr5:95324000-95326800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr5:95324200-95325000	Weak transcription	Gastric	stomach

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