Variant report

Variant	rs13402099
Chromosome Location	chr2:46947440-46947441
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46944884..46947962-chr2:46948655..46951641,3	K562	blood:
2	chr2:46924560..46926945-chr2:46947357..46950271,2	MCF-7	breast:
3	chr2:46924864..46926962-chr2:46945163..46948583,3	MCF-7	breast:
4	chr2:46946506..46948828-chr2:46997236..46999160,2	K562	blood:

Variant related genes	Relation type
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10187320	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10192254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196768	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10204610	0.85[ASN][1000 genomes]
rs10221923	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10439427	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10439469	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12151534	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12329330	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs13391877	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13412085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13420535	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13421701	0.87[AFR][1000 genomes]
rs13424717	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13426735	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13432741	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs17770970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17771838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35750425	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
6	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46934000-46947800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:46942400-46947800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:46942800-46948600	Enhancers	NH-A	brain
4	chr2:46943800-46947800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:46943800-46948000	Weak transcription	Fetal Stomach	stomach
6	chr2:46944200-46948200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr2:46944400-46947800	Weak transcription	Left Ventricle	heart
8	chr2:46944400-46947800	Weak transcription	Pancreas	Pancrea
9	chr2:46944600-46947800	Weak transcription	Fetal Muscle Leg	muscle
10	chr2:46945000-46948000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:46945200-46947600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:46945200-46947800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:46945200-46947800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:46945200-46947800	Weak transcription	Aorta	Aorta
15	chr2:46945200-46947800	Weak transcription	Right Atrium	heart
16	chr2:46945200-46948600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr2:46945400-46947600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:46945400-46947800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:46945400-46947800	Weak transcription	Adipose Nuclei	Adipose
20	chr2:46945400-46947800	Weak transcription	Liver	Liver
21	chr2:46945400-46947800	Weak transcription	Ovary	ovary
22	chr2:46945400-46947800	Weak transcription	Psoas Muscle	Psoas
23	chr2:46945400-46947800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:46945400-46947800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:46945400-46947800	Enhancers	NHDF-Ad	bronchial
26	chr2:46945400-46950800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:46945400-46952600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr2:46945400-46953400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:46945400-46985400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:46945600-46947800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:46945600-46948000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr2:46945800-46947800	Enhancers	NHLF	lung
33	chr2:46945800-46948600	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr2:46946000-46948600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:46946200-46947800	Enhancers	GM12878-XiMat	blood
36	chr2:46946200-46948000	Enhancers	Primary B cells from cord blood	blood
37	chr2:46946200-46948200	Enhancers	NHEK	skin
38	chr2:46946200-46949600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr2:46946400-46947600	Enhancers	HSMM	muscle
40	chr2:46946400-46947800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:46946400-46948000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:46946400-46948400	Enhancers	HepG2	liver
43	chr2:46946400-46948600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:46946400-46949000	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr2:46946400-46949000	Enhancers	Fetal Heart	heart
46	chr2:46946600-46947800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr2:46946600-46948200	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr2:46946600-46948200	Enhancers	Fetal Thymus	thymus
49	chr2:46946600-46948200	Enhancers	Right Ventricle	heart
50	chr2:46946600-46948200	Flanking Active TSS	A549	lung

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