Variant report

Variant	rs13393889
Chromosome Location	chr2:149055810-149055811
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	EGR1	chr2:149055754-149056180	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ENSG00000224007	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10211100	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12691782	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12691784	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13413027	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13427839	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16828556	0.82[ASN][1000 genomes]
rs4972354	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567802	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7605678	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9653191	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9750419	0.82[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	nsv869146	chr2:148787051-149060763	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv2753542	chr2:149004714-149268503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1012275	chr2:149031668-149316793	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv523090	chr2:149037012-149110873	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13393889	ACVR2A	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:149012800-149096000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:149017400-149062800	Weak transcription	Fetal Lung	lung
3	chr2:149017400-149070600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:149017600-149060800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:149026000-149070400	Weak transcription	Fetal Intestine Small	intestine
6	chr2:149031400-149079000	Weak transcription	Left Ventricle	heart
7	chr2:149041600-149058200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:149042200-149070600	Weak transcription	Ovary	ovary
9	chr2:149042600-149057600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:149042800-149058000	Weak transcription	HSMM	muscle
11	chr2:149043400-149063600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:149045600-149060600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:149045600-149070600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:149050600-149062600	Weak transcription	Fetal Stomach	stomach
15	chr2:149050800-149056400	Weak transcription	Thymus	Thymus
16	chr2:149052800-149058400	Weak transcription	Aorta	Aorta
17	chr2:149053000-149060600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:149053800-149057800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:149054600-149057800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:149054800-149057800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:149055200-149056000	Strong transcription	Primary T cells from cord blood	blood
22	chr2:149055200-149072400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr2:149055400-149056000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr2:149055400-149056000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr2:149055400-149056600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:149055400-149058600	Weak transcription	Brain Germinal Matrix	brain
27	chr2:149055600-149056000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:149055600-149056000	Enhancers	H9 Cell Line	embryonic stem cell
29	chr2:149055600-149056000	Strong transcription	Primary B cells from cord blood	blood
30	chr2:149055600-149056000	Enhancers	NH-A	brain
31	chr2:149055600-149056200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:149055600-149056600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:149055600-149060200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:149055800-149056000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr2:149055800-149056000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:149055800-149056000	Enhancers	Esophagus	oesophagus
37	chr2:149055800-149056400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr2:149055800-149059200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:149055800-149059400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:149055800-149059600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:149055800-149059600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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