Variant report

Variant	rs4671962
Chromosome Location	chr2:54798896-54798897
allele	A/T
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	chr2:54782556..54791633-chr2:54796824..54803982,19	MCF-7	breast:
2	chr2:54796760..54799671-chr2:54800450..54802770,2	K562	blood:
3	chr2:54783962..54788714-chr2:54796833..54801765,9	K562	blood:
4	chr2:54793317..54796723-chr2:54797852..54801262,4	MCF-7	breast:
5	chr2:54797362..54799747-chr2:54810321..54813282,3	K562	blood:
6	chr2:54797516..54799490-chr2:54803547..54805303,2	K562	blood:
7	chr2:54796611..54799496-chr2:54810522..54814074,3	MCF-7	breast:
8	chr2:54797826..54799514-chr2:54816272..54818809,2	MCF-7	breast:
9	chr2:54781728..54792106-chr2:54796721..54808716,28	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10164713	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10165641	0.86[EUR][1000 genomes]
rs1027950	0.83[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs1052788	0.85[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs1052820	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1112919	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs12463484	0.84[EUR][1000 genomes]
rs12467653	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12473338	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12475342	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12475598	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12476489	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12615589	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12622708	0.83[EUR][1000 genomes]
rs13387476	0.89[EUR][1000 genomes]
rs17416284	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs2007020	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs3796012	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3817163	0.96[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs4283459	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4519565	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs4557016	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4567979	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671223	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs4671224	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4671227	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671229	0.83[CEU][hapmap]
rs4671952	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs4671959	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671964	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4671965	0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs59871921	0.81[EUR][1000 genomes]
rs60294349	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545428	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs6545433	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]
rs6705756	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs6738725	0.88[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs6739099	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67457439	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68134840	0.83[EUR][1000 genomes]
rs72618663	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72618664	0.84[ASN][1000 genomes]
rs9309255	0.96[CEU][hapmap];0.88[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
rs4671962	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54789800-54801400	Enhancers	Liver	Liver
2	chr2:54791200-54801200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr2:54793000-54799800	Enhancers	Stomach Mucosa	stomach
4	chr2:54794400-54804200	Weak transcription	Ovary	ovary
5	chr2:54795000-54799400	Enhancers	Fetal Heart	heart
6	chr2:54795200-54799000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:54795200-54799800	Enhancers	Fetal Intestine Large	intestine
8	chr2:54795200-54802200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:54795400-54799200	Enhancers	HUVEC	blood vessel
10	chr2:54795400-54801400	Enhancers	Fetal Thymus	thymus
11	chr2:54795600-54799400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr2:54795600-54802400	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr2:54795800-54799200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr2:54795800-54799400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:54795800-54799400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr2:54795800-54799400	Flanking Active TSS	A549	lung
17	chr2:54795800-54800000	Enhancers	NHLF	lung
18	chr2:54795800-54801200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:54795800-54801800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr2:54795800-54801800	Enhancers	Fetal Kidney	kidney
21	chr2:54795800-54802400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:54795800-54803000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr2:54795800-54803200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr2:54795800-54803400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr2:54795800-54807000	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr2:54795800-54807600	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr2:54796000-54799400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr2:54796000-54799400	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr2:54796000-54801200	Enhancers	Thymus	Thymus
30	chr2:54796000-54801600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:54796000-54801600	Enhancers	Brain Substantia Nigra	brain
32	chr2:54796000-54801800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:54796000-54802000	Enhancers	Brain Cingulate Gyrus	brain
34	chr2:54796000-54802000	Enhancers	Fetal Lung	lung
35	chr2:54796000-54802200	Enhancers	HSMMtube	muscle
36	chr2:54796000-54802400	Enhancers	Brain Hippocampus Middle	brain
37	chr2:54796000-54802600	Enhancers	HMEC	breast
38	chr2:54796000-54802800	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr2:54796000-54804400	Enhancers	Adipose Nuclei	Adipose
40	chr2:54796000-54807600	Enhancers	Brain Angular Gyrus	brain
41	chr2:54796200-54799000	Enhancers	Left Ventricle	heart
42	chr2:54796200-54800400	Enhancers	Fetal Muscle Leg	muscle
43	chr2:54796200-54801400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:54796200-54801400	Enhancers	Placenta	Placenta
45	chr2:54796200-54801600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr2:54796200-54801800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr2:54796200-54806200	Enhancers	Right Atrium	heart
48	chr2:54796200-54806400	Enhancers	Brain Anterior Caudate	brain
49	chr2:54796200-54806800	Enhancers	Pancreas	Pancrea
50	chr2:54796400-54802200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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