Variant report

Variant	rs17054838
Chromosome Location	chr13:37621119-37621120
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	chr13:37573255..37575883-chr13:37618152..37622818,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALG5-4	chr13:37621001-37621738	NONHSAT033241

Variant related genes	Relation type
ENSG00000120699	Chromatin interaction
ENSG00000120697	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10507444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1199997	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199998	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200000	1.00[ASN][1000 genomes]
rs1200001	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200002	1.00[ASN][1000 genomes]
rs1200003	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1336165	1.00[ASN][1000 genomes]
rs17054770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17054775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17054789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];1.00[ASN][1000 genomes]
rs17054790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs17054792	0.91[AFR][1000 genomes]
rs17054829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054835	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17054925	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054972	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924421	1.00[ASN][1000 genomes]
rs2181788	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2769542	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4624036	1.00[ASN][1000 genomes]
rs57719094	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59899061	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59901477	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608385	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs6563506	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73533924	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73543820	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74045176	0.91[AFR][1000 genomes]
rs7986414	0.84[EUR][1000 genomes]
rs7991565	0.84[EUR][1000 genomes]
rs8001410	1.00[ASN][1000 genomes]
rs9315475	1.00[CHB][hapmap]
rs9547703	1.00[CHB][hapmap]
rs9547704	1.00[CHB][hapmap]
rs9594177	0.81[AFR][1000 genomes]
rs9594184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs9603124	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];1.00[ASN][1000 genomes]
rs9603150	1.00[CHB][hapmap]

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	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37575400-37631200	Weak transcription	Stomach Mucosa	stomach
2	chr13:37576200-37623800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr13:37576400-37623800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr13:37576600-37623000	Strong transcription	Liver	Liver
5	chr13:37576600-37625800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr13:37576800-37621200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr13:37576800-37623200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr13:37577000-37623000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr13:37577000-37623400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr13:37577000-37624400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr13:37577200-37623200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr13:37577200-37625200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr13:37577200-37625800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr13:37577200-37625800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr13:37577600-37623600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr13:37581800-37622800	Strong transcription	Dnd41	blood
17	chr13:37583000-37622800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr13:37583000-37623400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr13:37583200-37622600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr13:37586800-37623400	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr13:37587000-37622200	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr13:37587800-37622600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr13:37588400-37622400	Strong transcription	Adipose Nuclei	Adipose
24	chr13:37589200-37625800	Strong transcription	Fetal Thymus	thymus
25	chr13:37589400-37622600	Strong transcription	Placenta	Placenta
26	chr13:37589600-37623800	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr13:37592200-37622600	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr13:37594600-37622400	Strong transcription	Primary B cells from cord blood	blood
29	chr13:37599600-37623000	Strong transcription	HSMM	muscle
30	chr13:37601800-37625200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr13:37602200-37621600	Strong transcription	Primary T cells from cord blood	blood
32	chr13:37602800-37622200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr13:37604200-37623600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr13:37604400-37622200	Strong transcription	NH-A	brain
35	chr13:37604400-37622800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr13:37604800-37622800	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr13:37604800-37623600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr13:37605000-37622800	Strong transcription	Osteobl	bone
39	chr13:37606800-37632400	Weak transcription	Hela-S3	cervix
40	chr13:37607800-37631000	Weak transcription	Pancreas	Pancrea
41	chr13:37608400-37624000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr13:37608800-37631800	Weak transcription	Psoas Muscle	Psoas
43	chr13:37609600-37622600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr13:37610000-37631000	Weak transcription	Lung	lung
45	chr13:37610000-37632200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr13:37610200-37623200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr13:37610200-37626000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr13:37610600-37632000	Weak transcription	Small Intestine	intestine
49	chr13:37610800-37625800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr13:37611400-37621400	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links