Variant report

Variant	rs2141579
Chromosome Location	chr3:133181936-133181937
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:133169398..133190840-chr3:133288286..133298861,41	MCF-7	breast:
2	chr3:133166486..133169051-chr3:133181517..133184490,2	MCF-7	breast:
3	chr3:133179819..133183044-chr3:133290517..133294355,4	MCF-7	breast:
4	chr3:133180499..133182281-chr3:133188502..133190705,2	MCF-7	breast:
5	chr3:133180327..133181853-chr3:133181928..133184881,2	MCF-7	breast:
6	chr3:133179746..133182359-chr3:133292415..133294343,2	K562	blood:
7	chr3:133173610..133177245-chr3:133178784..133182075,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249993	Chromatin interaction
ENSG00000170819	Chromatin interaction
ENSG00000091527	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10512901	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11715830	0.82[ASN][1000 genomes]
rs13069027	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2737717	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34763711	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7612063	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs931099	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	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
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2141579	BFSP2	cis	multi-tissue	Pritchard
rs2141579	BFSP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 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	chr3:133177200-133185800	Enhancers	Fetal Thymus	thymus
3	chr3:133178600-133185600	Weak transcription	Left Ventricle	heart
4	chr3:133178800-133186800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:133179000-133182400	Weak transcription	Fetal Kidney	kidney
6	chr3:133179000-133187000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:133179400-133185600	Enhancers	GM12878-XiMat	blood
8	chr3:133179600-133187400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:133180000-133182000	Weak transcription	Placenta	Placenta
10	chr3:133180000-133182200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:133180000-133182200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:133180000-133182200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:133180000-133182400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:133180000-133182400	Weak transcription	Colonic Mucosa	Colon
15	chr3:133180000-133183400	Weak transcription	Stomach Mucosa	stomach
16	chr3:133180000-133185600	Weak transcription	Right Atrium	heart
17	chr3:133180000-133187000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:133180000-133191000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:133180400-133182200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr3:133180400-133182200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:133180400-133182200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:133180400-133182200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:133180400-133182200	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:133180400-133185200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:133180400-133185400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:133180400-133185600	Weak transcription	Esophagus	oesophagus
27	chr3:133180600-133182200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:133180600-133182200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:133180600-133182200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:133180600-133183400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:133180600-133185200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr3:133180600-133185600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:133180600-133185800	Weak transcription	HSMMtube	muscle
34	chr3:133180800-133182200	Weak transcription	NHEK	skin
35	chr3:133180800-133182400	Weak transcription	HepG2	liver
36	chr3:133181000-133182000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:133181000-133182200	Weak transcription	Primary T cells from cord blood	blood
38	chr3:133181000-133182200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:133181000-133182200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:133181000-133183200	Enhancers	Thymus	Thymus
41	chr3:133181200-133183600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:133181400-133182000	Weak transcription	Hela-S3	cervix
43	chr3:133181400-133182200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:133181400-133184400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:133181400-133191400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr3:133181600-133182000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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