Variant report

Variant	rs3213710
Chromosome Location	chr4:15717321-15717322
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	chr4:15655671..15658131-chr4:15716646..15719360,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11724635	0.82[CEU][hapmap]
rs35519415	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4541502	0.92[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4631042	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4698412	0.82[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]

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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3213710	BST1	cis	multi-tissue	Pritchard
rs3213710	LOC285550	cis	multi-tissue	Pritchard

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15697600-15723600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:15705000-15735200	Weak transcription	Lung	lung
3	chr4:15705200-15720400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:15705200-15720600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:15705200-15731000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:15705400-15718800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:15705400-15727400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:15705800-15719400	Weak transcription	Spleen	Spleen
9	chr4:15706000-15727800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:15707400-15742800	Weak transcription	Primary B cells from cord blood	blood
11	chr4:15708800-15720200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr4:15708800-15739400	Weak transcription	Ovary	ovary
13	chr4:15709200-15719600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr4:15709400-15731800	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:15710000-15718800	Weak transcription	Hela-S3	cervix
16	chr4:15710000-15723600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:15711400-15720200	Weak transcription	HepG2	liver
18	chr4:15711800-15719400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr4:15712200-15717400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:15714600-15717600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:15714600-15717800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:15714600-15720200	Weak transcription	Fetal Intestine Small	intestine
23	chr4:15715400-15719200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:15715600-15718600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:15715800-15717800	Enhancers	Fetal Brain Male	brain
26	chr4:15715800-15720200	Enhancers	Fetal Stomach	stomach
27	chr4:15715800-15721600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr4:15716000-15717600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:15716000-15720000	Enhancers	NHLF	lung
30	chr4:15716200-15718000	Weak transcription	Placenta	Placenta
31	chr4:15716200-15723400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:15716400-15718000	Weak transcription	Brain Angular Gyrus	brain
33	chr4:15716400-15718400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:15716400-15723000	Weak transcription	A549	lung
35	chr4:15716600-15717400	Weak transcription	Brain Substantia Nigra	brain
36	chr4:15716600-15717600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:15716600-15717600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr4:15716600-15718200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:15716600-15718400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:15716600-15718600	Weak transcription	Fetal Muscle Leg	muscle
41	chr4:15716600-15719200	Weak transcription	Fetal Kidney	kidney
42	chr4:15716600-15719800	Enhancers	Osteobl	bone
43	chr4:15716600-15725200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:15716800-15717800	Weak transcription	HSMMtube	muscle
45	chr4:15716800-15718000	Weak transcription	NH-A	brain
46	chr4:15716800-15718200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr4:15716800-15718800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr4:15716800-15720600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr4:15716800-15727600	Weak transcription	Brain Anterior Caudate	brain
50	chr4:15717000-15718000	Weak transcription	Brain Germinal Matrix	brain

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