Variant report

Variant	rs12713012
Chromosome Location	chr2:48904550-48904551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48904136..48905986-chr2:48910089..48911674,2	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10198501	0.81[CHD][hapmap]
rs10208754	0.82[CHB][hapmap];0.81[CHD][hapmap];0.84[MEX][hapmap]
rs10209208	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10495955	0.90[CHD][hapmap];0.84[GIH][hapmap]
rs11125178	0.86[ASN][1000 genomes]
rs11125179	1.00[CHB][hapmap]
rs11676166	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11677854	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11678398	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11679449	0.82[AMR][1000 genomes]
rs11685904	0.90[CHD][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];0.80[AMR][1000 genomes]
rs11689544	0.88[MEX][hapmap]
rs11691408	1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.88[ASN][1000 genomes]
rs11694191	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11892581	1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.83[ASN][1000 genomes]
rs11899239	0.95[ASN][1000 genomes]
rs11901588	0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs12469348	0.80[LWK][hapmap]
rs12987494	0.80[AMR][1000 genomes]
rs12992138	0.82[AMR][1000 genomes]
rs12992918	0.82[AMR][1000 genomes]
rs12993815	0.82[AMR][1000 genomes]
rs12995714	0.83[ASN][1000 genomes]
rs12997569	0.90[CHD][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap]
rs13014919	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13022553	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13024367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1404051	0.88[ASN][1000 genomes]
rs1464728	0.81[MKK][hapmap]
rs1464729	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1589749	0.90[CHD][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];0.80[AMR][1000 genomes]
rs17326209	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs17326251	0.85[CHB][hapmap]
rs1916838	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs1996969	0.81[CHD][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2056581	0.83[ASN][1000 genomes]
rs2293275	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs2349099	0.90[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.80[AMR][1000 genomes]
rs2349101	1.00[CHB][hapmap]
rs28666758	0.98[ASN][1000 genomes]
rs34003293	0.83[ASN][1000 genomes]
rs34124947	0.82[AMR][1000 genomes]
rs34205206	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34378457	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34393991	0.80[AMR][1000 genomes]
rs34757099	0.80[AMR][1000 genomes]
rs34790224	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35125065	1.00[ASN][1000 genomes]
rs35362799	0.82[EUR][1000 genomes]
rs35422158	0.80[AMR][1000 genomes]
rs35461667	0.82[AMR][1000 genomes]
rs35501278	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35540486	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35737133	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35866214	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3792240	0.82[EUR][1000 genomes]
rs3792243	0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs3792246	1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs4429518	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62137505	0.80[AMR][1000 genomes]
rs62137532	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6706586	0.86[ASN][1000 genomes]
rs6720650	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6730379	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6734199	1.00[ASN][1000 genomes]
rs6738387	0.90[CHD][hapmap]
rs6741840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6746530	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6746623	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6747475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6747688	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6749600	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6760849	0.88[ASN][1000 genomes]
rs7559006	0.95[ASN][1000 genomes]
rs7562038	0.95[ASN][1000 genomes]
rs7572902	0.95[ASN][1000 genomes]
rs7583310	0.83[ASN][1000 genomes]
rs7587112	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv581776	chr2:48763382-48913019	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv874004	chr2:48838955-48904550	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12713012	STON1-GTF2A1L	cis	cerebellum	SCAN
rs12713012	STON1-GTF2A1L	cis	Esophagus Mucosa	GTEx
rs12713012	SIX3	cis	cerebellum	SCAN
rs12713012	STON1-GTF2A1L	cis	parietal	SCAN
rs12713012	STON1-GTF2A1L	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48863000-48919600	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:48869800-48915400	Weak transcription	Adipose Nuclei	Adipose
3	chr2:48874200-48919600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:48898800-48920200	Weak transcription	Ovary	ovary
5	chr2:48899400-48906800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:48904400-48905200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:48904400-48905200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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