Variant report

Variant	rs4076027
Chromosome Location	chr12:85671807-85671808
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	REST	chr12:85671681-85672258	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr12:85671434-85672003	H1-neurons	neurons:	n/a	n/a
3	SIN3AK20	chr12:85671622-85672340	PFSK-1	brain:	n/a	n/a
4	TAF1	chr12:85671636-85672348	PFSK-1	brain:	n/a	n/a
5	CTBP2	chr12:85671727-85674564	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr12:85671717-85672001	PFSK-1	brain:	n/a	n/a
7	YY1	chr12:85671633-85672443	H1-hESC	embryonic stem cell:	n/a	n/a
8	SUZ12	chr12:85670810-85673700	H1-hESC	embryonic stem cell:	n/a	n/a
9	FOXP2	chr12:85671730-85672037	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr12:85671305-85679401	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr12:85671530-85677070	PFSK-1	brain:	n/a	n/a

Variant related genes	Relation type
ALX1	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1011728	0.80[EUR][1000 genomes]
rs10779155	0.84[EUR][1000 genomes]
rs10862966	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10862967	0.80[EUR][1000 genomes]
rs10862968	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10862969	0.82[EUR][1000 genomes]
rs11116771	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11608487	0.83[EUR][1000 genomes]
rs11608773	0.80[EUR][1000 genomes]
rs12315575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810608	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs1512732	0.96[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1512733	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1512735	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2660454	0.82[ASN][1000 genomes]
rs2660455	0.82[ASN][1000 genomes]
rs2660459	0.82[ASN][1000 genomes]
rs2708498	0.82[ASN][1000 genomes]
rs34688666	0.80[EUR][1000 genomes]
rs35338871	0.83[EUR][1000 genomes]
rs35388734	0.83[EUR][1000 genomes]
rs4074726	0.83[EUR][1000 genomes]
rs4374010	0.85[AFR][1000 genomes]
rs4761130	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6539889	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7306109	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7316291	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7486483	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7488598	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040452	chr12:85179586-85747907	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv1792335	chr12:85321249-86003609	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv899388	chr12:85427691-85766847	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1040622	chr12:85502226-85693132	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv541558	chr12:85502226-85693132	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv559662	chr12:85544429-85734069	Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv817242	chr12:85622245-86069213	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv2761757	chr12:85626466-85741934	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv899392	chr12:85638089-85734069	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv533923	chr12:85647133-85713608	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1054573	chr12:85658602-86235433	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1035600	chr12:85661373-86235433	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:85670400-85672600	Weak transcription	Hela-S3	cervix
2	chr12:85671600-85672000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
3	chr12:85671600-85672000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
4	chr12:85671600-85672200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
5	chr12:85671600-85673800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr12:85671800-85672000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:85671800-85672000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
8	chr12:85671800-85672000	Bivalent Enhancer	Fetal Kidney	kidney
9	chr12:85671800-85672600	Bivalent Enhancer	Brain Germinal Matrix	brain
10	chr12:85671800-85672800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:85671800-85672800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
12	chr12:85671800-85672800	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:85671800-85673000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
14	chr12:85671800-85673000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:85671800-85673000	ZNF genes & repeats	Spleen	Spleen
16	chr12:85671800-85673400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
17	chr12:85671800-85673600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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