Variant report

Variant	rs12214056
Chromosome Location	chr6:25060863-25060864
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	FOXA1	chr6:25060795-25061120	HepG2	liver:	n/a	n/a
2	STAT3	chr6:25060855-25060980	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:25060649..25063407-chr6:25066068..25067636,2	K562	blood:
2	chr6:25059218..25061939-chr6:25066118..25068353,2	K562	blood:
3	chr6:25056745..25058998-chr6:25059205..25062203,2	K562	blood:

Variant related genes	Relation type
ENSG00000223623	TF binding region
ENSG00000223623	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10946746	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1555431	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs303034	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs303898	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs303899	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs303900	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs4568441	0.95[YRI][hapmap]
rs460400	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6916014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9356960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9358829	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358831	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9379708	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379711	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379712	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9379714	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9393611	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461094	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12214056	HIST1H2AG	cis	parietal	SCAN
rs12214056	CMAH	cis	parietal	SCAN
rs12214056	BTN3A1	cis	cerebellum	SCAN
rs12214056	SLC17A4	cis	cerebellum	SCAN
rs12214056	CMAH	cis	lymphoblastoid	seeQTL
rs12214056	CMAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25046000-25062400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:25051200-25061600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:25054200-25061400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:25054200-25061400	Weak transcription	Lung	lung
5	chr6:25055000-25061400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:25055400-25061200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:25055400-25064200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:25056600-25061400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:25056600-25061600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:25057600-25061400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:25057600-25080400	Weak transcription	Thymus	Thymus
12	chr6:25057800-25061000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:25057800-25061400	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:25057800-25061600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:25057800-25061600	Weak transcription	Fetal Thymus	thymus
16	chr6:25057800-25062800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:25057800-25062800	Weak transcription	Placenta	Placenta
18	chr6:25058000-25061200	Weak transcription	NHDF-Ad	bronchial
19	chr6:25058000-25061400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:25058000-25061600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:25058000-25061600	Weak transcription	Fetal Stomach	stomach
22	chr6:25059400-25062000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:25059600-25062600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr6:25060200-25061400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:25060400-25063000	Enhancers	Adipose Nuclei	Adipose
26	chr6:25060600-25061600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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