Variant report

Variant	rs13420838
Chromosome Location	chr2:172261877-172261878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172261014..172263381-chr2:172264531..172266240,2	MCF-7	breast:
2	chr2:172260491..172264264-chr2:172264585..172267651,3	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10171164	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10177689	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10186304	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192493	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195990	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198915	0.86[AMR][1000 genomes]
rs10202883	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10210332	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13386613	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13388963	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13395084	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13396824	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13402901	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13414723	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28608023	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663293	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4566333	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58367130	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58808521	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59235233	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59318451	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59449823	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59599047	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60523677	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62181354	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73976149	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73976150	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73976153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73976158	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73976177	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7580497	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973419	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973709	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172222200-172289600	Weak transcription	Gastric	stomach
2	chr2:172238000-172272400	Weak transcription	Fetal Intestine Large	intestine
3	chr2:172238800-172272400	Weak transcription	Primary T cells from cord blood	blood
4	chr2:172248000-172266000	Weak transcription	Left Ventricle	heart
5	chr2:172248600-172265400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:172254600-172265400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:172256200-172264000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:172256800-172263400	Weak transcription	Fetal Brain Male	brain
9	chr2:172257000-172266000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:172257600-172266000	Weak transcription	Aorta	Aorta
11	chr2:172258000-172262800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:172258200-172265200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:172258200-172265400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:172258600-172272400	Weak transcription	A549	lung
15	chr2:172259200-172262200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:172259400-172265400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:172259400-172272200	Weak transcription	Fetal Intestine Small	intestine
18	chr2:172259600-172262200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:172259600-172262200	Enhancers	Hela-S3	cervix
20	chr2:172259600-172262200	Enhancers	NHEK	skin
21	chr2:172259800-172262000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:172259800-172262200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:172259800-172262800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:172259800-172266000	Weak transcription	Esophagus	oesophagus
25	chr2:172260000-172271000	Weak transcription	K562	blood
26	chr2:172260200-172262000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:172260200-172272200	Weak transcription	HepG2	liver
28	chr2:172260800-172265600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:172261000-172263000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:172261000-172264000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:172261000-172265600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:172261000-172266000	Enhancers	Primary B cells from peripheral blood	blood
33	chr2:172261200-172265000	Enhancers	Primary B cells from cord blood	blood
34	chr2:172261400-172266000	Weak transcription	Small Intestine	intestine
35	chr2:172261600-172262000	Enhancers	GM12878-XiMat	blood
36	chr2:172261600-172264400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:172261600-172265000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:172261600-172265400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:172261600-172265600	Weak transcription	HSMMtube	muscle
40	chr2:172261600-172265800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:172261600-172266000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:172261600-172266000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:172261600-172266000	Weak transcription	Dnd41	blood
44	chr2:172261600-172266000	Weak transcription	NHLF	lung
45	chr2:172261600-172266200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:172261600-172277800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:172261800-172262800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:172261800-172265200	Weak transcription	HMEC	breast
49	chr2:172261800-172265800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:172261800-172266000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links