Variant report

Variant	rs10055677
Chromosome Location	chr5:114973671-114973672
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	BATF	chr5:114973387-114974304	GM12878	blood:	n/a	n/a
2	JUND	chr5:114973669-114974102	GM12878	blood:	n/a	chr5:114974015-114974025 chr5:114974016-114974024 chr5:114974016-114974023 chr5:114974016-114974024
3	RELA	chr5:114973420-114974270	GM12891	blood:	n/a	n/a
4	RELA	chr5:114973641-114974253	GM19099	blood:	n/a	n/a
5	NFATC1	chr5:114973557-114974179	GM12878	blood:	n/a	n/a
6	MEF2A	chr5:114973569-114974058	GM12878	blood:	n/a	chr5:114974016-114974024
7	BCLAF1	chr5:114973637-114974167	GM12878	blood:	n/a	chr5:114973970-114973979
8	EBF1	chr5:114973671-114974304	GM12878	blood:	n/a	n/a
9	PAX5	chr5:114973599-114974226	GM12878	blood:	n/a	n/a
10	MEF2A	chr5:114973604-114974200	GM12878	blood:	n/a	chr5:114974016-114974024
11	NFIC	chr5:114973521-114974368	GM12878	blood:	n/a	n/a
12	STAT5A	chr5:114973607-114974115	GM12878	blood:	n/a	n/a
13	CTCF	chr5:114973667-114973874	GM12878	blood:	n/a	n/a
14	STAT5A	chr5:114973597-114974224	GM12878	blood:	n/a	n/a
15	BCL11A	chr5:114973641-114974202	GM12878	blood:	n/a	chr5:114973970-114973979
16	NFYB	chr5:114973636-114974233	GM12878	blood:	n/a	chr5:114974006-114974020
17	RCOR1	chr5:114973396-114974334	GM12878	blood:	n/a	n/a
18	EBF1	chr5:114973365-114974284	GM12878	blood:	n/a	n/a
19	JUND	chr5:114973594-114974197	GM12878	blood:	n/a	chr5:114974015-114974025 chr5:114974016-114974024 chr5:114974016-114974023 chr5:114974016-114974024
20	RELA	chr5:114973511-114974197	GM12878	blood:	n/a	n/a
21	PML	chr5:114973502-114974333	GM12878	blood:	n/a	chr5:114974014-114974023
22	TBL1XR1	chr5:114973657-114974130	GM12878	blood:	n/a	n/a
23	RUNX3	chr5:114973435-114974246	GM12878	blood:	n/a	n/a
24	NFIC	chr5:114973513-114974354	GM12878	blood:	n/a	n/a
25	MTA3	chr5:114973347-114974225	GM12878	blood:	n/a	n/a
26	EP300	chr5:114973671-114974152	GM12878	blood:	n/a	n/a
27	FOXM1	chr5:114973587-114974227	GM12878	blood:	n/a	n/a
28	ATF2	chr5:114973554-114974262	GM12878	blood:	n/a	n/a
29	EBF1	chr5:114973665-114974230	GM12878	blood:	n/a	n/a
30	ATF2	chr5:114973594-114974279	GM12878	blood:	n/a	n/a
31	BHLHE40	chr5:114973381-114974114	GM12878	blood:	n/a	n/a
32	SP1	chr5:114973630-114974166	GM12878	blood:	n/a	n/a
33	IRF4	chr5:114973554-114974281	GM12878	blood:	n/a	n/a
34	RUNX3	chr5:114973567-114974244	GM12878	blood:	n/a	n/a
35	NFATC1	chr5:114973589-114974187	GM12878	blood:	n/a	n/a
36	BATF	chr5:114973623-114974160	GM12878	blood:	n/a	n/a
37	MTA3	chr5:114973667-114974211	GM12878	blood:	n/a	n/a
38	CUX1	chr5:114973659-114974077	GM12878	blood:	n/a	n/a
39	FOXM1	chr5:114973591-114974299	GM12878	blood:	n/a	n/a
40	IKZF1	chr5:114973598-114974217	GM12878	blood:	n/a	n/a
41	CEBPB	chr5:114973523-114974259	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:114971626..114974342-chr5:115178110..115179917,2	K562	blood:
2	chr5:114970607..114974645-chr5:114975238..114977621,3	K562	blood:
3	chr5:114970889..114973875-chr5:114975413..114978406,3	MCF-7	breast:
4	chr5:114972992..114975914-chr5:115155123..115157177,2	MCF-7	breast:

Variant related genes	Relation type
TMED7	TF binding region
ENSG00000177879	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs13164545	0.96[CEU][hapmap];0.80[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13186296	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs171774	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2303747	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs256941	0.97[ASN][1000 genomes]
rs256942	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256944	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs256945	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs256947	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256948	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256949	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256950	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256951	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256952	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256953	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256954	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256955	0.87[CHB][hapmap]
rs256962	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs256964	1.00[CEU][hapmap];0.96[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs256967	0.92[EUR][1000 genomes]
rs256969	0.92[EUR][1000 genomes]
rs256988	0.92[EUR][1000 genomes]
rs256991	0.92[EUR][1000 genomes]
rs256993	0.92[EUR][1000 genomes]
rs256997	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs256998	0.92[EUR][1000 genomes]
rs377290	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3822579	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs400570	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs413059	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs415577	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs416234	0.94[ASN][1000 genomes]
rs424434	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs428191	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4920967	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62371215	0.81[ASN][1000 genomes]
rs698365	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs698366	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs698367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712550	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs712551	0.95[ASN][1000 genomes]
rs7702283	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702869	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7702881	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs790824	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs790825	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9326969	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10055677	SEMA6A	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114970400-114974000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:114970600-114974400	Weak transcription	Liver	Liver
3	chr5:114971600-114975400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:114971800-114976800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:114972000-114975600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr5:114972400-114974000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:114972800-114974400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:114972800-114976800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:114972800-114977000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:114973000-114974200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:114973400-114974200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:114973400-114974200	Enhancers	NHDF-Ad	bronchial
13	chr5:114973600-114973800	Flanking Active TSS	GM12878-XiMat	blood
14	chr5:114973600-114974600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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