Variant report

Variant	rs456816
Chromosome Location	chr6:25059241-25059242
allele	A/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	STAT3	chr6:25059167-25059367	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25059218..25061939-chr6:25066118..25068353,2	K562	blood:
2	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: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1002596	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs159988	1.00[CHB][hapmap]
rs16890104	0.82[CHB][hapmap]
rs186237	0.85[AFR][1000 genomes]
rs2028973	0.82[CHB][hapmap]
rs2166682	0.93[CEU][hapmap]
rs2166683	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2394363	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs302973	1.00[CHB][hapmap]
rs302983	0.82[CHB][hapmap]
rs302991	1.00[CHB][hapmap]
rs303000	0.85[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs303006	1.00[CHB][hapmap]
rs303009	1.00[CHB][hapmap]
rs303016	0.82[CHB][hapmap]
rs303018	0.82[CHB][hapmap]
rs303026	0.82[CHB][hapmap]
rs303877	0.85[AFR][1000 genomes]
rs303878	0.81[AFR][1000 genomes]
rs3792970	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs3792971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs3792986	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3818268	0.93[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs392852	1.00[CHB][hapmap]
rs4711077	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4711078	0.84[EUR][1000 genomes]
rs6906102	0.93[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs715426	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs715427	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7740661	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs7740668	0.93[CEU][hapmap]
rs9295646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9295647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9356961	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9358833	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9379717	0.82[EUR][1000 genomes]
rs9393613	0.86[CHB][hapmap]
rs9393617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs9654585	0.84[EUR][1000 genomes];0.83[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs456816	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs456816	CMAH	cis	multi-tissue	Pritchard

Chromatin state (count:30 , 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	chr6:25055000-25060400	Weak transcription	Adipose Nuclei	Adipose
6	chr6:25055000-25061400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:25055400-25061200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:25055400-25064200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:25056600-25061400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:25056600-25061600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:25056800-25059600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:25057000-25059400	Enhancers	Primary B cells from cord blood	blood
13	chr6:25057600-25059400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr6:25057600-25061400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:25057600-25080400	Weak transcription	Thymus	Thymus
16	chr6:25057800-25061000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:25057800-25061400	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:25057800-25061600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:25057800-25061600	Weak transcription	Fetal Thymus	thymus
20	chr6:25057800-25062800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr6:25057800-25062800	Weak transcription	Placenta	Placenta
22	chr6:25058000-25060600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:25058000-25061200	Weak transcription	NHDF-Ad	bronchial
24	chr6:25058000-25061400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:25058000-25061600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:25058000-25061600	Weak transcription	Fetal Stomach	stomach
27	chr6:25058800-25059600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr6:25058800-25059600	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr6:25059200-25060200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr6:25059200-25060600	Weak transcription	Primary B cells from peripheral blood	blood

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