Variant report

Variant	rs6439409
Chromosome Location	chr3:133185294-133185295
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: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2370247	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628262	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9289448	0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6439409	BFSP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:50 , 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	chr3:133179000-133187000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:133179400-133185600	Enhancers	GM12878-XiMat	blood
7	chr3:133179600-133187400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:133180000-133185600	Weak transcription	Right Atrium	heart
9	chr3:133180000-133187000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:133180000-133191000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:133180400-133185400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:133180400-133185600	Weak transcription	Esophagus	oesophagus
13	chr3:133180600-133185600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:133180600-133185800	Weak transcription	HSMMtube	muscle
15	chr3:133181400-133191400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:133182200-133187200	Enhancers	Primary B cells from cord blood	blood
17	chr3:133182200-133188800	Enhancers	Primary B cells from peripheral blood	blood
18	chr3:133182400-133185800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:133182600-133185400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:133182600-133185600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:133182600-133185600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:133182600-133185600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:133182600-133185600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:133182600-133192600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:133183000-133185600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:133183000-133185600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:133183000-133185600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:133183000-133185600	Weak transcription	Colonic Mucosa	Colon
29	chr3:133183000-133185600	Weak transcription	Placenta	Placenta
30	chr3:133183000-133185600	Weak transcription	NHEK	skin
31	chr3:133183000-133188000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:133183000-133192800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:133183600-133186800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:133183800-133186800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:133183800-133187000	Weak transcription	HSMM	muscle
36	chr3:133183800-133191800	Weak transcription	Small Intestine	intestine
37	chr3:133184200-133187400	Enhancers	Thymus	Thymus
38	chr3:133184400-133185600	Enhancers	Primary T cells from cord blood	blood
39	chr3:133184400-133185800	Weak transcription	HepG2	liver
40	chr3:133184600-133185600	Weak transcription	Spleen	Spleen
41	chr3:133184600-133187000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:133184600-133190200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:133185000-133185400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr3:133185000-133186000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr3:133185000-133186600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:133185000-133188400	Enhancers	Fetal Muscle Leg	muscle
47	chr3:133185200-133186000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr3:133185200-133186000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr3:133185200-133186200	Enhancers	Primary T cells fromperipheralblood	blood
50	chr3:133185200-133187200	Enhancers	Primary T helper naive cells from peripheral blood	blood

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