Variant report

Variant	rs11871944
Chromosome Location	chr17:67057288-67057289
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	MYC	chr17:67057149-67057349	MCF10A-Er-Src	breast:	n/a	chr17:67057206-67057217 chr17:67057205-67057220 chr17:67057203-67057218
2	USF1	chr17:67057055-67057344	SK-N-SH_RA	brain:	n/a	n/a
3	SIN3AK20	chr17:67057121-67057380	PFSK-1	brain:	n/a	n/a
4	EBF1	chr17:67056990-67057299	GM12878	blood:	n/a	chr17:67057156-67057167

Variant related genes	Relation type
ABCA9	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10512523	0.95[CHB][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs1076401	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11077858	1.00[ASW][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap]
rs11077859	1.00[ASW][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs11077860	1.00[ASW][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs11077884	0.84[CEU][hapmap]
rs11453	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs11657541	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11659114	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11871766	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs12325889	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs1541470	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs16973495	0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs2079808	0.86[ASN][1000 genomes]
rs2302291	0.80[CEU][hapmap];0.82[CHD][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2302292	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs2302293	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs2302294	1.00[ASW][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs4968983	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4968993	0.98[ASN][1000 genomes]
rs62082714	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6501947	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs71357712	0.81[ASN][1000 genomes]
rs7207125	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs7215642	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7217543	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7218871	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs8066758	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs8067578	0.99[ASN][1000 genomes]
rs8068236	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs8070285	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs9789039	0.81[ASN][1000 genomes]
rs9902602	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833526	chr17:66980758-67137034	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11871944	ABCA6	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67041400-67072600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr17:67048400-67057600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr17:67053800-67066800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr17:67055400-67058000	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr17:67055400-67058000	Enhancers	Brain Substantia Nigra	brain
6	chr17:67055600-67057800	Enhancers	Brain Germinal Matrix	brain
7	chr17:67055600-67058000	Enhancers	Brain Anterior Caudate	brain
8	chr17:67055800-67057600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:67055800-67057600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr17:67056000-67058200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr17:67056200-67058000	Enhancers	Osteobl	bone
12	chr17:67056200-67058200	Enhancers	Brain Hippocampus Middle	brain
13	chr17:67056200-67075200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr17:67056600-67057800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr17:67056600-67058000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr17:67056800-67057400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr17:67056800-67057400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr17:67056800-67057800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:67056800-67058200	Enhancers	Brain Angular Gyrus	brain
20	chr17:67056800-67058200	Enhancers	Brain Cingulate Gyrus	brain
21	chr17:67057000-67057400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr17:67057000-67057400	Enhancers	GM12878-XiMat	blood
23	chr17:67057000-67057400	Enhancers	HUVEC	blood vessel
24	chr17:67057000-67058000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr17:67057000-67058200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:67057000-67058400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr17:67057000-67058600	Enhancers	NHDF-Ad	bronchial
28	chr17:67057000-67062400	Weak transcription	Fetal Muscle Leg	muscle
29	chr17:67057200-67057400	Flanking Active TSS	Fetal Kidney	kidney
30	chr17:67057200-67057400	Weak transcription	Ovary	ovary
31	chr17:67057200-67058000	Enhancers	Fetal Stomach	stomach
32	chr17:67057200-67058200	Enhancers	Adipose Nuclei	Adipose
33	chr17:67057200-67058200	Enhancers	Fetal Lung	lung
34	chr17:67057200-67058200	Enhancers	NHLF	lung
35	chr17:67057200-67058400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr17:67057200-67058800	Weak transcription	Primary monocytes fromperipheralblood	blood

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