Variant report

Variant	rs13412887
Chromosome Location	chr2:46589487-46589488
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46523497..46525893-chr2:46586751..46589747,2	MCF-7	breast:
2	chr2:46589429..46592507-chr2:46593401..46595603,3	K562	blood:
3	chr2:46541093..46544345-chr2:46588792..46591987,3	K562	blood:
4	chr2:46586164..46589641-chr2:46590092..46593590,4	K562	blood:

Variant related genes	Relation type
ENSG00000116016	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1868084	0.83[JPT][hapmap]
rs4145836	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv916169	chr2:46310963-46622603	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13412887	BTG4	trans	cerebellum	SCAN
rs13412887	MCFD2	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46568000-46596600	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:46572600-46590600	Strong transcription	NHEK	skin
3	chr2:46573200-46613000	Strong transcription	Hela-S3	cervix
4	chr2:46573800-46591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:46574000-46589600	Strong transcription	A549	lung
6	chr2:46574200-46589600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:46574200-46590600	Strong transcription	Placenta Amnion	Placenta Amnion
8	chr2:46574400-46590400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:46574600-46607200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:46574800-46613000	Weak transcription	HSMM	muscle
11	chr2:46578600-46590400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:46578800-46590800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:46580000-46594600	Weak transcription	Psoas Muscle	Psoas
14	chr2:46580400-46589600	Strong transcription	Duodenum Mucosa	Duodenum
15	chr2:46580600-46589600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:46580600-46597200	Weak transcription	Fetal Heart	heart
17	chr2:46580800-46589800	Strong transcription	HUVEC	blood vessel
18	chr2:46581000-46589800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:46581200-46597000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:46581800-46589600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:46582800-46589800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:46582800-46590200	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr2:46583000-46590400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr2:46583000-46591000	Weak transcription	Fetal Kidney	kidney
25	chr2:46583000-46591000	Strong transcription	Ovary	ovary
26	chr2:46583200-46591000	Strong transcription	Gastric	stomach
27	chr2:46584400-46591000	Weak transcription	K562	blood
28	chr2:46584600-46589600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:46585000-46593200	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:46585200-46594600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:46585400-46590200	Weak transcription	NHDF-Ad	bronchial
32	chr2:46585400-46592000	Weak transcription	Brain Substantia Nigra	brain
33	chr2:46585400-46593200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:46585400-46594000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:46585600-46592600	Weak transcription	Brain Anterior Caudate	brain
36	chr2:46585600-46593200	Weak transcription	Brain Angular Gyrus	brain
37	chr2:46586200-46591200	Strong transcription	HepG2	liver
38	chr2:46586600-46604000	Weak transcription	HSMMtube	muscle
39	chr2:46587000-46589600	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:46587200-46589600	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:46587200-46590000	Genic enhancers	Placenta	Placenta
42	chr2:46587200-46591000	Strong transcription	Aorta	Aorta
43	chr2:46587400-46589600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:46587400-46589600	Strong transcription	Fetal Intestine Small	intestine
45	chr2:46587400-46590200	Strong transcription	Esophagus	oesophagus
46	chr2:46587400-46590400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:46587400-46590600	Genic enhancers	Left Ventricle	heart
48	chr2:46587400-46591000	Strong transcription	Fetal Stomach	stomach
49	chr2:46587400-46591200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:46587600-46591200	Weak transcription	Fetal Muscle Leg	muscle

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