Variant report

Variant	rs2737717
Chromosome Location	chr3:133185834-133185835
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	chr3:133169398..133190840-chr3:133288286..133298861,41	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091527	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10512901	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10935064	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs13069027	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1881918	0.95[CHB][hapmap]
rs2078262	0.86[CHB][hapmap]
rs2141579	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276737	0.81[CHB][hapmap]
rs34763711	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7612063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs931099	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[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	nsv1006289	chr3:133137664-133186808	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv1829199	chr3:133158065-133213047	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv877505	chr3:133167363-133235272	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2737717	BFSP2	cis	lymphoblastoid	seeQTL
rs2737717	BFSP2	cis	Lymphoblastoid	GTEx
rs2737717	BFSP2	Cis_1M	lymphoblastoid	RTeQTL
rs2737717	ENSG00000170819	cis	multi-tissue	Pritchard
rs2737717	BFSP2	cis	multi-tissue	Pritchard

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133161000-133191000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:133178800-133186800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:133179000-133187000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:133179600-133187400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:133180000-133187000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:133180000-133191000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:133181400-133191400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:133182200-133187200	Enhancers	Primary B cells from cord blood	blood
9	chr3:133182200-133188800	Enhancers	Primary B cells from peripheral blood	blood
10	chr3:133182600-133192600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:133183000-133188000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:133183000-133192800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:133183600-133186800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:133183800-133186800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:133183800-133187000	Weak transcription	HSMM	muscle
16	chr3:133183800-133191800	Weak transcription	Small Intestine	intestine
17	chr3:133184200-133187400	Enhancers	Thymus	Thymus
18	chr3:133184600-133187000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:133184600-133190200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:133185000-133186000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr3:133185000-133186600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:133185000-133188400	Enhancers	Fetal Muscle Leg	muscle
23	chr3:133185200-133186000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr3:133185200-133186000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr3:133185200-133186200	Enhancers	Primary T cells fromperipheralblood	blood
26	chr3:133185200-133187200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr3:133185400-133186200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:133185400-133186800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr3:133185600-133186000	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr3:133185600-133186000	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr3:133185600-133186000	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr3:133185600-133186000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:133185600-133186000	Enhancers	Colon Smooth Muscle	Colon
34	chr3:133185600-133186000	Enhancers	Right Ventricle	heart
35	chr3:133185600-133186200	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:133185600-133186200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:133185600-133186200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:133185600-133186200	Enhancers	Duodenum Mucosa	Duodenum
39	chr3:133185600-133186200	Enhancers	Esophagus	oesophagus
40	chr3:133185600-133186200	Enhancers	Placenta	Placenta
41	chr3:133185600-133186200	Enhancers	Left Ventricle	heart
42	chr3:133185600-133186200	Enhancers	Right Atrium	heart
43	chr3:133185600-133186400	Enhancers	Primary hematopoietic stem cells	blood
44	chr3:133185600-133186400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:133185600-133186400	Enhancers	Adipose Nuclei	Adipose
46	chr3:133185600-133186400	Enhancers	Fetal Muscle Trunk	muscle
47	chr3:133185600-133186400	Enhancers	Psoas Muscle	Psoas
48	chr3:133185600-133186400	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr3:133185600-133186400	Enhancers	Spleen	Spleen
50	chr3:133185600-133186400	Flanking Active TSS	GM12878-XiMat	blood

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