Variant report

Variant	rs12586560
Chromosome Location	chr14:78111633-78111634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78111581..78113767-chr14:78114274..78115867,2	K562	blood:
2	chr14:78110088..78114382-chr14:78173079..78175530,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100601	Chromatin interaction
ENSG00000119705	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10873310	0.94[ASN][1000 genomes]
rs11159282	0.94[ASN][1000 genomes]
rs11159285	0.97[ASN][1000 genomes]
rs11620917	0.85[CHD][hapmap]
rs11625133	0.96[YRI][hapmap]
rs12050437	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050439	0.98[ASN][1000 genomes]
rs12432127	0.97[ASN][1000 genomes]
rs12435993	0.82[CHD][hapmap]
rs12590445	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12590759	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12590776	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12878099	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs12879146	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12880698	0.84[ASN][1000 genomes]
rs12881338	0.91[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.94[ASN][1000 genomes]
rs12881530	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12886970	0.98[ASN][1000 genomes]
rs12889224	1.00[ASN][1000 genomes]
rs12898009	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2886123	0.85[CHD][hapmap]
rs34140630	1.00[ASN][1000 genomes]
rs34567686	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35636868	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243658	0.82[CHD][hapmap]
rs4899664	0.94[ASN][1000 genomes]
rs4903619	0.97[ASN][1000 genomes]
rs4903620	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67838524	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71428789	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7149026	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7155602	0.83[CEU][hapmap]
rs8004037	0.96[ASN][1000 genomes]
rs8021379	0.85[CHD][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription 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	33 gene(s)	inside rSNPs	diseases
5	esv2757575	chr14:78104897-78212462	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34940	chr14:78104897-78222798	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv521287	chr14:78108003-78211225	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12586560	SPTLC2	cis	cerebellum	SCAN
rs12586560	RPS6KL1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78108800-78118000	Weak transcription	Psoas Muscle	Psoas
2	chr14:78109000-78112000	Weak transcription	Stomach Mucosa	stomach
3	chr14:78109000-78113400	Weak transcription	Fetal Intestine Large	intestine
4	chr14:78109000-78113800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr14:78111400-78112000	Enhancers	K562	blood
6	chr14:78111400-78112800	Enhancers	Placenta	Placenta
7	chr14:78111600-78112000	Weak transcription	Duodenum Mucosa	Duodenum

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