Variant report

Variant	rs2370247
Chromosome Location	chr3:133186741-133186742
allele	G/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	POLR2A	chr3:133185398-133186995	Raji	blood:	n/a	n/a
2	RUNX3	chr3:133186629-133187738	GM12878	blood:	n/a	n/a

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
BFSP2	TF binding region
ENSG00000091527	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2370246	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs6439409	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628262	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9289448	0.90[JPT][hapmap];0.83[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2370247	BFSP2	cis	multi-tissue	Pritchard
rs2370247	BFSP2	Cis_1M	lymphoblastoid	RTeQTL

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	chr3:133178800-133186800	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	chr3:133185000-133188400	Enhancers	Fetal Muscle Leg	muscle
21	chr3:133185200-133187200	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr3:133185400-133186800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr3:133185600-133186800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr3:133185600-133187200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:133185800-133188800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr3:133185800-133194200	Weak transcription	Gastric	stomach
27	chr3:133186000-133186800	Weak transcription	HepG2	liver
28	chr3:133186000-133187400	Enhancers	Primary T cells from cord blood	blood
29	chr3:133186000-133187400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:133186000-133192800	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:133186000-133193800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr3:133186000-133195600	Weak transcription	Right Ventricle	heart
33	chr3:133186200-133187400	Weak transcription	Left Ventricle	heart
34	chr3:133186200-133188000	Weak transcription	Placenta	Placenta
35	chr3:133186200-133192800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:133186200-133193400	Weak transcription	Right Atrium	heart
37	chr3:133186200-133193800	Weak transcription	Esophagus	oesophagus
38	chr3:133186400-133186800	Weak transcription	Adipose Nuclei	Adipose
39	chr3:133186400-133186800	Weak transcription	HSMMtube	muscle
40	chr3:133186400-133187400	Weak transcription	Psoas Muscle	Psoas
41	chr3:133186400-133188800	Enhancers	Fetal Thymus	thymus
42	chr3:133186400-133190400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:133186400-133192000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:133186400-133193800	Weak transcription	Spleen	Spleen
45	chr3:133186600-133186800	Enhancers	Pancreas	Pancrea
46	chr3:133186600-133187600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:133186600-133187600	Flanking Active TSS	GM12878-XiMat	blood

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