Variant report

Variant	rs2279531
Chromosome Location	chr3:112356770-112356771
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	chr3:112354988..112357166-chr3:112709171..112711334,2	MCF-7	breast:
2	chr3:112354638..112357493-chr3:112357624..112362114,5	K562	blood:

Variant related genes	Relation type
ENSG00000163607	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000272844	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs3842905	0.80[EUR][1000 genomes]
rs6438086	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6438087	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6794305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6807798	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7611898	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9683135	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9815819	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9821338	0.89[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers 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 miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2279531	BOC	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112342600-112359600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:112343400-112358000	Weak transcription	Pancreas	Pancrea
3	chr3:112345200-112359400	Weak transcription	Esophagus	oesophagus
4	chr3:112348200-112358400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:112348600-112357200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:112348800-112358400	Weak transcription	Hela-S3	cervix
7	chr3:112351400-112358600	Transcr. at gene 5' and 3'	Osteobl	bone
8	chr3:112351800-112357800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:112352600-112358400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:112353000-112358600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:112353000-112358600	Weak transcription	Fetal Brain Male	brain
12	chr3:112353800-112357200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr3:112354000-112357000	Active TSS	Brain Hippocampus Middle	brain
14	chr3:112354000-112359000	Flanking Active TSS	NH-A	brain
15	chr3:112354000-112359200	Weak transcription	Fetal Brain Female	brain
16	chr3:112354000-112360600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:112354200-112357800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:112354200-112358000	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr3:112354200-112358200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:112354400-112356800	Active TSS	NHLF	lung
21	chr3:112354400-112357800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:112354400-112357800	Active TSS	HSMMtube	muscle
23	chr3:112354400-112359000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:112354600-112359400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:112354800-112357200	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:112354800-112357600	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr3:112354800-112358600	Weak transcription	NHEK	skin
28	chr3:112354800-112359000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:112354800-112359000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:112354800-112359000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:112354800-112360000	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr3:112355000-112358600	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr3:112355000-112358800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:112355000-112359000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:112355200-112357000	Active TSS	Right Atrium	heart
36	chr3:112355200-112358400	Weak transcription	HUVEC	blood vessel
37	chr3:112355400-112358400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:112355400-112359600	Active TSS	Colonic Mucosa	Colon
39	chr3:112355600-112356800	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr3:112355600-112356800	Flanking Active TSS	Fetal Lung	lung
41	chr3:112355600-112357000	Active TSS	Left Ventricle	heart
42	chr3:112355600-112358600	Enhancers	Ovary	ovary
43	chr3:112355800-112357200	Active TSS	NHDF-Ad	bronchial
44	chr3:112355800-112357400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:112355800-112357600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:112355800-112358000	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr3:112355800-112360200	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr3:112356000-112356800	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr3:112356000-112356800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:112356000-112357000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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