Variant report

Variant	rs411817
Chromosome Location	chr5:94977654-94977655
allele	C/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	MAFK	chr5:94977567-94977810	HepG2	liver:	n/a	chr5:94977668-94977683
2	FOXA1	chr5:94977425-94977821	T-47D	breast:	n/a	n/a
3	RFX5	chr5:94977611-94977811	HepG2	liver:	n/a	n/a
4	NR3C1	chr5:94977484-94977869	A549	lung:	n/a	n/a
5	FOXA1	chr5:94977461-94977844	HepG2	liver:	n/a	n/a
6	FOXA1	chr5:94977420-94977846	HepG2	liver:	n/a	n/a
7	MAZ	chr5:94977572-94977821	K562	blood:	n/a	n/a
8	JUND	chr5:94977481-94977899	HepG2	liver:	n/a	chr5:94977721-94977730
9	JUND	chr5:94977431-94977893	K562	blood:	n/a	chr5:94977721-94977730
10	MAFF	chr5:94977553-94977822	HepG2	liver:	n/a	chr5:94977666-94977684
11	MAFK	chr5:94977638-94977838	K562	blood:	n/a	chr5:94977668-94977683
12	GATA3	chr5:94977434-94977961	T-47D	breast:	n/a	chr5:94977564-94977572 chr5:94977454-94977462
13	NR3C1	chr5:94977480-94977817	A549	lung:	n/a	chr5:94977482-94977499
14	FOXA2	chr5:94977488-94977779	HepG2	liver:	n/a	n/a
15	NR3C1	chr5:94977496-94977869	A549	lung:	n/a	n/a
16	GATA3	chr5:94977448-94978069	MCF-7	breast:	n/a	chr5:94977564-94977572 chr5:94977454-94977462
17	RCOR1	chr5:94977532-94978046	K562	blood:	n/a	n/a
18	GATA3	chr5:94977439-94977924	T-47D	breast:	n/a	chr5:94977564-94977572 chr5:94977454-94977462
19	SIN3AK20	chr5:94977282-94978035	MCF-7	breast:	n/a	n/a
20	TBP	chr5:94977486-94977789	HepG2	liver:	n/a	n/a
21	ARID3A	chr5:94977503-94977803	HepG2	liver:	n/a	n/a
22	FOXA1	chr5:94977512-94977870	T-47D	breast:	n/a	n/a
23	MAFK	chr5:94977491-94977844	HepG2	liver:	n/a	chr5:94977668-94977683

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:94977116..95012475-chr5:95055682..95079552,215	K562	blood:

Variant related genes	Relation type
RFESD	TF binding region
ENSG00000250240	Chromatin interaction
ENSG00000164292	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10063774	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10075777	0.84[AFR][1000 genomes]
rs13166682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13172592	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13179768	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs150548	0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[ASN][1000 genomes]
rs150549	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs150550	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs213507	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs213508	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213509	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213510	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs213511	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs213512	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs213880	0.90[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs213885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213887	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213888	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs412026	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs440342	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4869245	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6865873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890832	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598955	chr5:94903453-95136019	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv598960	chr5:94975592-94988482	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs411817	RHOBTB3	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94968200-94979800	Weak transcription	Primary T cells from cord blood	blood
2	chr5:94974800-94979800	Weak transcription	GM12878-XiMat	blood
3	chr5:94975200-94979200	Enhancers	Pancreas	Pancrea
4	chr5:94976000-94982400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:94976600-94978200	Enhancers	Fetal Intestine Small	intestine
6	chr5:94976600-94978600	Enhancers	Fetal Intestine Large	intestine
7	chr5:94976800-94978200	Enhancers	Stomach Mucosa	stomach
8	chr5:94976800-94978400	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr5:94976800-94982200	Enhancers	Liver	Liver
10	chr5:94977000-94977800	Enhancers	Duodenum Mucosa	Duodenum
11	chr5:94977200-94977800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr5:94977200-94978000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:94977400-94977800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:94977400-94977800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:94977400-94977800	Flanking Active TSS	HepG2	liver
16	chr5:94977400-94978000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr5:94977400-94978200	Enhancers	K562	blood
18	chr5:94977400-94978400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:94977600-94977800	Enhancers	Aorta	Aorta
20	chr5:94977600-94977800	Enhancers	NHEK	skin
21	chr5:94977600-94979800	Weak transcription	NHLF	lung
22	chr5:94977600-94980400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr5:94977600-94982200	Weak transcription	Right Atrium	heart
24	chr5:94977600-94982200	Weak transcription	HSMM	muscle

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