Variant report

Variant	rs3809208
Chromosome Location	chr12:20847996-20847997
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	POLR2A	chr12:20847929-20848576	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
SLCO1C1	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12578492	1.00[ASN][1000 genomes]
rs12580616	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12580628	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12581970	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1399937	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1399938	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3794270	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55661764	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56174957	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57238599	0.94[ASN][1000 genomes]
rs57312777	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59508686	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60480171	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61579575	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61623220	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6487131	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6487132	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67017312	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67028347	1.00[ASN][1000 genomes]
rs72658756	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72658759	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72658760	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72658761	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7296571	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7303066	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7310399	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314545	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7316120	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73240436	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73240439	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73240441	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74065151	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74065172	0.82[ASN][1000 genomes]
rs74065173	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs74066232	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs74066238	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs74066258	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7956705	0.81[EUR][1000 genomes]
rs7960786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7970439	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7970863	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7975280	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7975334	1.00[ASN][1000 genomes]
rs7978760	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1043890	chr12:20659151-21309993	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv541410	chr12:20659151-21309993	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1054997	chr12:20682009-21292602	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv557704	chr12:20842041-20893980	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20838800-20849800	Weak transcription	Hela-S3	cervix
2	chr12:20846800-20848000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr12:20846800-20848200	Enhancers	Adipose Nuclei	Adipose
4	chr12:20847000-20848200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:20847000-20848400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:20847000-20849400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr12:20847200-20848800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr12:20847400-20848400	Weak transcription	Fetal Stomach	stomach
9	chr12:20847600-20849400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr12:20847800-20848000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:20847800-20848400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:20847800-20849400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr12:20847800-20849800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr12:20847800-20850000	Active TSS	Brain Anterior Caudate	brain

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