Variant report

Variant	rs1571256
Chromosome Location	chr13:48671081-48671082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr13:48670594-48671294	HepG2	liver:	n/a	n/a
2	FOXA1	chr13:48670982-48671191	T-47D	breast:	n/a	n/a
3	NANOG	chr13:48670876-48671157	H1-hESC	embryonic stem cell:	n/a	n/a
4	ARID3A	chr13:48670686-48671246	HepG2	liver:	n/a	n/a
5	TEAD4	chr13:48670673-48671367	HepG2	liver:	n/a	n/a
6	HNF4A	chr13:48670739-48671170	HepG2	liver:	n/a	n/a
7	GTF2F1	chr13:48671055-48671103	H1-hESC	embryonic stem cell:	n/a	n/a
8	HDAC2	chr13:48670728-48671225	HepG2	liver:	n/a	chr13:48671138-48671147
9	FOXA1	chr13:48670674-48671265	HepG2	liver:	n/a	n/a
10	NANOG	chr13:48670838-48671112	H1-hESC	embryonic stem cell:	n/a	n/a
11	FOXA1	chr13:48670611-48671336	HepG2	liver:	n/a	n/a
12	FOXA1	chr13:48670757-48671217	HepG2	liver:	n/a	n/a
13	EP300	chr13:48670791-48671082	HepG2	liver:	n/a	n/a
14	FOXA1	chr13:48671015-48671238	T-47D	breast:	n/a	n/a
15	EP300	chr13:48670618-48671220	HepG2	liver:	n/a	n/a
16	FOXA2	chr13:48670623-48671290	HepG2	liver:	n/a	n/a
17	ESR1	chr13:48670659-48671256	T-47D	breast:	n/a	n/a
18	ESR1	chr13:48670673-48671096	T-47D	breast:	n/a	n/a
19	TEAD4	chr13:48670835-48671248	H1-hESC	embryonic stem cell:	n/a	n/a
20	ESR1	chr13:48670706-48671351	T-47D	breast:	n/a	n/a
21	CEBPB	chr13:48670696-48671206	HepG2	liver:	n/a	n/a
22	GATA3	chr13:48670846-48671190	T-47D	breast:	n/a	n/a
23	SP1	chr13:48670647-48671217	HepG2	liver:	n/a	n/a
24	ESR1	chr13:48670693-48671094	T-47D	breast:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48573763..48575874-chr13:48669435..48671518,2	MCF-7	breast:

No data

Variant related genes	Relation type
MED4	TF binding region
ENSG00000227848	Chromatin interaction
ENSG00000136143	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11616639	0.87[ASN][1000 genomes]
rs1410117	0.94[ASN][1000 genomes]
rs1927213	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2094192	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2104480	1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2148246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2148938	1.00[CHB][hapmap];1.00[JPT][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]
rs2406709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2406797	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4294712	0.94[ASN][1000 genomes]
rs4369555	0.95[JPT][hapmap]
rs4941623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4942748	0.98[ASN][1000 genomes]
rs56399021	0.91[ASN][1000 genomes]
rs7324484	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7326363	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7333247	0.87[ASN][1000 genomes]
rs7336214	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8001243	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9526442	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9526443	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9526445	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526447	0.94[ASN][1000 genomes]
rs9526449	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526451	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9534888	0.95[JPT][hapmap]
rs9534931	0.83[ASN][1000 genomes]
rs9534932	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9534933	0.91[ASN][1000 genomes]
rs9534937	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9534939	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs9534943	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9534944	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];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9534945	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9534946	0.93[ASN][1000 genomes]
rs9534947	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9534948	0.93[ASN][1000 genomes]
rs9534949	0.89[ASN][1000 genomes]
rs9534950	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9534951	0.92[ASN][1000 genomes]
rs9534952	0.94[ASN][1000 genomes]
rs9534957	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534961	0.85[ASN][1000 genomes]
rs9534965	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs9562802	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9567987	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9567991	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9567994	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs9568000	0.89[ASN][1000 genomes]
rs9568014	0.86[CHB][hapmap];0.81[JPT][hapmap]

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	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1571256	FAM194B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48669400-48674200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:48669600-48671200	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr13:48669600-48671400	Enhancers	Stomach Mucosa	stomach
4	chr13:48669800-48671400	Enhancers	Liver	Liver
5	chr13:48669800-48671400	Enhancers	Fetal Kidney	kidney
6	chr13:48669800-48685400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr13:48670000-48671600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr13:48670400-48671200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr13:48670400-48671600	Flanking Active TSS	HepG2	liver
10	chr13:48670600-48671200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr13:48670600-48671400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr13:48670800-48671400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr13:48671000-48671400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr13:48671000-48672000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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