Variant report

Variant	rs6545433
Chromosome Location	chr2:54817833-54817834
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54783987..54787753-chr2:54814113..54820814,10	K562	blood:
2	chr2:54816128..54819257-chr2:54823273..54825897,3	MCF-7	breast:
3	chr2:54814029..54817875-chr2:54846911..54850562,3	K562	blood:
4	chr2:54810337..54813834-chr2:54815762..54818177,4	MCF-7	breast:
5	chr2:54815000..54820095-chr2:54820709..54825309,10	K562	blood:
6	chr2:54815707..54819448-chr2:54820160..54824681,7	K562	blood:
7	chr2:54815022..54818519-chr2:54825874..54828742,4	K562	blood:
8	chr2:54797826..54799514-chr2:54816272..54818809,2	MCF-7	breast:
9	chr2:54789266..54791330-chr2:54815899..54818560,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10164713	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10165641	0.85[EUR][1000 genomes]
rs1027950	0.82[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs1052788	0.80[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs1052820	0.92[CEU][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs1112919	0.88[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs12463484	0.83[EUR][1000 genomes]
rs12467653	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12473338	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12475342	0.81[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12475598	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12476489	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12615589	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12622708	0.82[EUR][1000 genomes]
rs13387476	0.87[EUR][1000 genomes]
rs17416284	0.92[CEU][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs2007020	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs3796012	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3817163	0.89[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4283459	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4519565	0.96[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs4557016	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4567979	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671223	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs4671224	0.96[CEU][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs4671227	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4671229	0.82[CEU][hapmap]
rs4671952	0.92[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4671959	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4671962	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671964	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671965	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59871921	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60294349	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545428	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs6545438	0.82[CHB][hapmap]
rs6705756	0.92[CEU][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs6738725	0.89[ASW][hapmap];0.84[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs6739099	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67457439	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68134840	0.83[EUR][1000 genomes]
rs72618663	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72618664	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9309255	0.92[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6545433	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54802200-54822600	Weak transcription	Esophagus	oesophagus
2	chr2:54804000-54822400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:54805600-54819800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:54807000-54826000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:54807200-54819800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:54807800-54818800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:54808800-54822800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:54809400-54821600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr2:54809600-54825800	Weak transcription	Brain Germinal Matrix	brain
11	chr2:54811400-54819400	Enhancers	Stomach Mucosa	stomach
12	chr2:54811600-54818400	Enhancers	Brain Substantia Nigra	brain
13	chr2:54811600-54819200	Enhancers	Fetal Heart	heart
14	chr2:54811800-54818800	Enhancers	Brain Hippocampus Middle	brain
15	chr2:54813200-54818000	Enhancers	Brain Cingulate Gyrus	brain
16	chr2:54813600-54818000	Enhancers	Brain Angular Gyrus	brain
17	chr2:54814000-54822800	Weak transcription	Ovary	ovary
18	chr2:54814200-54818200	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr2:54814200-54819600	Weak transcription	Fetal Stomach	stomach
20	chr2:54814400-54819800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr2:54814600-54818600	Enhancers	Small Intestine	intestine
22	chr2:54814600-54819400	Enhancers	Fetal Brain Male	brain
23	chr2:54814800-54818000	Enhancers	Duodenum Mucosa	Duodenum
24	chr2:54814800-54818400	Enhancers	Fetal Intestine Large	intestine
25	chr2:54814800-54819600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:54814800-54819800	Weak transcription	HSMMtube	muscle
27	chr2:54814800-54820000	Enhancers	Primary B cells from peripheral blood	blood
28	chr2:54815000-54818200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr2:54815000-54818400	Enhancers	Thymus	Thymus
30	chr2:54815000-54819000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:54815000-54819200	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr2:54815000-54819800	Weak transcription	Fetal Brain Female	brain
33	chr2:54815400-54818200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:54815400-54823400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:54815600-54818000	Enhancers	HMEC	breast
36	chr2:54815800-54818000	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr2:54816000-54820400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:54816200-54818000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr2:54816200-54830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:54816400-54818200	Flanking Active TSS	Liver	Liver
41	chr2:54816600-54818200	Enhancers	Adipose Nuclei	Adipose
42	chr2:54816600-54819000	Enhancers	Fetal Intestine Small	intestine
43	chr2:54816600-54819200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:54816600-54819200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr2:54816600-54822400	Weak transcription	Gastric	stomach
46	chr2:54816600-54822400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:54816600-54822600	Weak transcription	Colonic Mucosa	Colon
48	chr2:54816600-54828400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:54816800-54818000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:54816800-54818000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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