Variant report

Variant	rs931099
Chromosome Location	chr3:133179580-133179581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr3:133179482-133179719	T-47D	breast:	n/a	n/a
2	ZNF263	chr3:133179563-133180354	HEK293-T-REx	kidney:	n/a	chr3:133179875-133179896
3	FOXA2	chr3:133179489-133179711	HepG2	liver:	n/a	n/a
4	EBF1	chr3:133179424-133179673	GM12878	blood:	n/a	chr3:133179464-133179473 chr3:133179573-133179586 chr3:133179464-133179473
5	FOXA2	chr3:133179433-133179777	A549	lung:	n/a	n/a
6	SIN3AK20	chr3:133179411-133180784	MCF-7	breast:	n/a	n/a
7	EBF1	chr3:133179403-133179750	GM12878	blood:	n/a	chr3:133179464-133179473 chr3:133179573-133179586 chr3:133179464-133179473

No.	Distal block	Cell Line	Cell type
1	chr3:133169398..133190840-chr3:133288286..133298861,41	MCF-7	breast:
2	chr3:133167608..133169678-chr3:133177159..133179764,2	MCF-7	breast:
3	chr3:133179282..133181210-chr3:133205623..133208031,2	MCF-7	breast:
4	chr3:133161498..133163430-chr3:133177580..133180492,2	MCF-7	breast:
5	chr3:133178497..133180168-chr3:133538134..133540708,2	MCF-7	breast:
6	chr3:133179034..133181660-chr3:133249507..133251496,2	MCF-7	breast:
7	chr3:133153374..133155623-chr3:133178756..133181568,2	MCF-7	breast:
8	chr3:133173610..133177245-chr3:133178784..133182075,5	MCF-7	breast:

Variant related genes	Relation type
BFSP2-AS1	TF binding region
ENSG00000170819	Chromatin interaction
ENSG00000249993	Chromatin interaction
ENSG00000091527	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10512901	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10935064	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11715830	0.87[ASN][1000 genomes]
rs13069027	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1881918	0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs2078262	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2141579	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276737	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2737717	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]
rs2859679	0.80[ASN][1000 genomes]
rs34763711	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7612063	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv1007047	chr3:133137664-133181388	Enhancers Weak transcription Active TSS Bivalent Enhancer 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	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
3	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
4	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
5	nsv237800	chr3:133178030-133185521	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs931099	BFSP2	cis	multi-tissue	Pritchard
rs931099	BFSP2	cis	lymphoblastoid	seeQTL
rs931099	BFSP2	Cis_1M	lymphoblastoid	RTeQTL
rs931099	BFSP2	cis	Lymphoblastoid	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133161000-133191000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:133175000-133179600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:133177200-133185800	Enhancers	Fetal Thymus	thymus
4	chr3:133177400-133180600	Enhancers	Thymus	Thymus
5	chr3:133177600-133181600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:133177800-133179600	Enhancers	Esophagus	oesophagus
7	chr3:133177800-133180000	Enhancers	Fetal Stomach	stomach
8	chr3:133178000-133180800	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr3:133178200-133179600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:133178200-133180000	Enhancers	Adipose Nuclei	Adipose
11	chr3:133178200-133180000	Enhancers	Psoas Muscle	Psoas
12	chr3:133178200-133180000	Enhancers	Right Atrium	heart
13	chr3:133178200-133180400	Enhancers	Fetal Muscle Leg	muscle
14	chr3:133178200-133180600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr3:133178200-133181000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:133178200-133181400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr3:133178400-133180000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:133178400-133180000	Enhancers	Colonic Mucosa	Colon
19	chr3:133178400-133180000	Enhancers	Placenta	Placenta
20	chr3:133178400-133180000	Enhancers	Stomach Mucosa	stomach
21	chr3:133178400-133180600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:133178600-133179600	Weak transcription	A549	lung
23	chr3:133178600-133180000	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr3:133178600-133181200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:133178600-133185600	Weak transcription	Left Ventricle	heart
26	chr3:133178800-133181000	Enhancers	Placenta Amnion	Placenta Amnion
27	chr3:133178800-133186800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:133179000-133179800	Weak transcription	Aorta	Aorta
29	chr3:133179000-133180000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr3:133179000-133182400	Weak transcription	Fetal Kidney	kidney
31	chr3:133179000-133187000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:133179200-133179800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:133179200-133180800	Enhancers	HepG2	liver
34	chr3:133179200-133180800	Enhancers	NHEK	skin
35	chr3:133179200-133181000	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr3:133179400-133179600	Enhancers	Primary T cells from cord blood	blood
37	chr3:133179400-133180000	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr3:133179400-133180000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr3:133179400-133180000	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr3:133179400-133180000	Enhancers	HMEC	breast
41	chr3:133179400-133180200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:133179400-133180400	Enhancers	Primary T cells fromperipheralblood	blood
43	chr3:133179400-133180600	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr3:133179400-133180600	Enhancers	HSMMtube	muscle
45	chr3:133179400-133181000	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr3:133179400-133181000	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr3:133179400-133185600	Enhancers	GM12878-XiMat	blood

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