Variant report

Variant	rs507868
Chromosome Location	chr18:12538482-12538483
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12536897..12541681-chr18:12655290..12658805,7	MCF-7	breast:
2	chr18:12538466..12540869-chr18:12656904..12659683,2	K562	blood:

Variant related genes	Relation type
ENSG00000134278	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000128789	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1539813	1.00[CHB][hapmap]
rs16939680	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1785308	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1893212	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs1893213	0.80[CHB][hapmap]
rs2249830	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2542172	1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap]
rs2542174	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4796966	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap]
rs479860	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs514831	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs550613	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56328751	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs575093	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58135011	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60876158	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61542301	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61635631	0.84[AMR][1000 genomes]
rs62097130	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62097132	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62097145	0.80[ASN][1000 genomes]
rs8086774	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv2756075	chr18:12481377-12548970	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs507868	VAPA	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12478800-12551800	Weak transcription	Pancreas	Pancrea
2	chr18:12492200-12548600	Weak transcription	Fetal Kidney	kidney
3	chr18:12493000-12541200	Weak transcription	NHEK	skin
4	chr18:12493200-12551800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr18:12509400-12539200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr18:12511400-12551800	Weak transcription	Lung	lung
7	chr18:12516000-12553200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr18:12516400-12539000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr18:12516600-12555000	Weak transcription	Aorta	Aorta
10	chr18:12518600-12540000	Weak transcription	Adipose Nuclei	Adipose
11	chr18:12518600-12551800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr18:12520800-12543400	Weak transcription	Osteobl	bone
13	chr18:12520800-12551800	Weak transcription	Colon Smooth Muscle	Colon
14	chr18:12520800-12552000	Weak transcription	NHLF	lung
15	chr18:12521000-12539200	Weak transcription	Fetal Stomach	stomach
16	chr18:12521000-12542000	Weak transcription	Ovary	ovary
17	chr18:12521000-12542200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr18:12521000-12552200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr18:12521200-12538600	Weak transcription	Brain Germinal Matrix	brain
20	chr18:12525600-12540800	Weak transcription	Gastric	stomach
21	chr18:12526400-12541400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr18:12530600-12540000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr18:12530600-12541000	Weak transcription	HMEC	breast
24	chr18:12530600-12551600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr18:12532200-12540800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr18:12533200-12540000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr18:12533200-12542400	Weak transcription	Fetal Heart	heart
28	chr18:12533200-12551800	Weak transcription	HSMMtube	muscle
29	chr18:12533600-12543200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr18:12534000-12551800	Weak transcription	Fetal Brain Male	brain
31	chr18:12534600-12551600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr18:12535000-12544600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr18:12535200-12539000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr18:12535200-12543400	Weak transcription	HSMM	muscle
35	chr18:12535400-12540000	Weak transcription	Fetal Brain Female	brain
36	chr18:12537400-12542000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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