Variant report

Variant	rs13387476
Chromosome Location	chr2:54762985-54762986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54761550..54763887-chr2:54765151..54767469,2	K562	blood:
2	chr2:54760402..54763033-chr2:54763448..54765136,2	MCF-7	breast:
3	chr2:54759200..54761130-chr2:54762739..54764614,2	K562	blood:
4	chr2:54761267..54763626-chr2:54824184..54826863,2	K562	blood:
5	chr2:54761132..54763342-chr2:54783145..54786144,3	MCF-7	breast:
6	chr2:54761029..54763821-chr2:54783036..54786331,4	K562	blood:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10165641	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1112919	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12463484	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12467653	0.85[EUR][1000 genomes]
rs12473338	0.82[EUR][1000 genomes]
rs12475598	0.86[EUR][1000 genomes]
rs12476489	0.85[EUR][1000 genomes]
rs12477376	0.87[EUR][1000 genomes]
rs12615589	0.81[EUR][1000 genomes]
rs12622708	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4283459	0.88[EUR][1000 genomes]
rs4519565	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4557016	0.81[EUR][1000 genomes]
rs4567979	0.91[EUR][1000 genomes]
rs4671223	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4671224	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4671227	0.90[EUR][1000 genomes]
rs4671952	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671959	0.91[EUR][1000 genomes]
rs4671962	0.89[EUR][1000 genomes]
rs60294349	0.86[EUR][1000 genomes]
rs6545428	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545433	0.87[EUR][1000 genomes]
rs6717713	0.81[EUR][1000 genomes]
rs6717816	0.81[EUR][1000 genomes]
rs6739099	0.88[EUR][1000 genomes]
rs67457439	0.82[EUR][1000 genomes]
rs68134840	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9309255	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv528848	chr2:54758305-54777576	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13387476	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
2	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
4	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
7	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:54752000-54764600	Weak transcription	Gastric	stomach
9	chr2:54752200-54767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:54753800-54764800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr2:54753800-54768200	Strong transcription	Fetal Muscle Leg	muscle
13	chr2:54754400-54767800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:54754800-54767800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:54755000-54767600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:54756600-54764200	Weak transcription	Psoas Muscle	Psoas
17	chr2:54756800-54763200	Enhancers	Fetal Intestine Large	intestine
18	chr2:54756800-54767600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:54757000-54767800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
21	chr2:54757400-54766200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:54757400-54771000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
24	chr2:54758600-54772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:54759400-54763000	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr2:54759600-54763800	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr2:54759600-54764000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr2:54760200-54768800	Genic enhancers	Left Ventricle	heart
29	chr2:54760400-54764000	Weak transcription	Ovary	ovary
30	chr2:54760400-54769600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:54760600-54763000	Enhancers	Brain Cingulate Gyrus	brain
32	chr2:54760600-54763600	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr2:54760600-54763600	Strong transcription	HSMMtube	muscle
34	chr2:54760600-54765200	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:54760600-54766000	Weak transcription	Small Intestine	intestine
36	chr2:54760600-54767000	Weak transcription	NH-A	brain
37	chr2:54760800-54763000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr2:54760800-54763000	Genic enhancers	A549	lung
39	chr2:54760800-54763200	Genic enhancers	HepG2	liver
40	chr2:54760800-54764000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:54760800-54767800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:54761000-54763200	Genic enhancers	Fetal Intestine Small	intestine
43	chr2:54761000-54763400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:54761000-54763400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:54761000-54764800	Strong transcription	Fetal Stomach	stomach
46	chr2:54761000-54767000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:54761000-54769400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:54761200-54763000	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:54761200-54764000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:54761200-54768800	Strong transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links