Variant report

Variant	rs4671952
Chromosome Location	chr2:54760038-54760039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54759032..54761078-chr2:54799312..54800939,2	MCF-7	breast:
2	chr2:54196354..54198285-chr2:54758115..54760291,3	MCF-7	breast:
3	chr2:54758614..54760270-chr2:54799626..54801180,2	MCF-7	breast:
4	chr2:54759443..54762729-chr2:54766620..54769498,3	MCF-7	breast:
5	chr2:54752145..54754517-chr2:54758567..54761057,2	MCF-7	breast:
6	chr2:54759200..54761130-chr2:54762739..54764614,2	K562	blood:

Variant related genes	Relation type
ENSG00000068878	Chromatin interaction
ENSG00000228108	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10165641	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1027950	0.82[CEU][hapmap]
rs1052788	0.80[CEU][hapmap]
rs1052820	0.92[CEU][hapmap]
rs1112919	0.88[CEU][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs12463484	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12476489	0.82[EUR][1000 genomes]
rs12477376	0.89[EUR][1000 genomes]
rs12622708	0.88[EUR][1000 genomes]
rs13387476	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17045941	0.95[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs17416284	0.92[CEU][hapmap]
rs3817163	0.92[CEU][hapmap];0.82[GIH][hapmap]
rs4283459	0.82[EUR][1000 genomes]
rs4519565	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4567979	0.85[EUR][1000 genomes]
rs4671223	0.96[CEU][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs4671224	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671227	0.85[EUR][1000 genomes]
rs4671229	0.82[CEU][hapmap]
rs4671959	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs4671962	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs4671965	0.88[CEU][hapmap]
rs60294349	0.80[EUR][1000 genomes]
rs6545428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545433	0.92[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs6705756	0.92[CEU][hapmap]
rs6717713	0.82[EUR][1000 genomes]
rs6717816	0.82[EUR][1000 genomes]
rs6738725	0.84[CEU][hapmap]
rs6739099	0.82[EUR][1000 genomes]
rs68134840	0.90[EUR][1000 genomes]
rs9309255	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	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
3	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
5	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
rs4671952	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
2	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
5	chr2:54747000-54760600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:54747200-54761800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
10	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:54751000-54760200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:54752000-54760200	Weak transcription	Colonic Mucosa	Colon
13	chr2:54752000-54764600	Weak transcription	Gastric	stomach
14	chr2:54752200-54767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:54753800-54764800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr2:54753800-54768200	Strong transcription	Fetal Muscle Leg	muscle
18	chr2:54754000-54760200	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:54754400-54767800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:54754800-54767800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:54755000-54761000	Weak transcription	Right Ventricle	heart
22	chr2:54755000-54767600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:54755400-54762600	Enhancers	Placenta Amnion	Placenta Amnion
24	chr2:54755600-54761200	Weak transcription	Fetal Brain Male	brain
25	chr2:54756600-54764200	Weak transcription	Psoas Muscle	Psoas
26	chr2:54756800-54763200	Enhancers	Fetal Intestine Large	intestine
27	chr2:54756800-54767600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:54757000-54761000	Enhancers	Fetal Intestine Small	intestine
29	chr2:54757000-54767800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
31	chr2:54757200-54761200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:54757400-54760400	Weak transcription	Fetal Kidney	kidney
33	chr2:54757400-54761200	Weak transcription	Fetal Brain Female	brain
34	chr2:54757400-54766200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:54757400-54771000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:54757800-54762000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:54758000-54760200	Enhancers	NH-A	brain
38	chr2:54758000-54760400	Enhancers	HUVEC	blood vessel
39	chr2:54758000-54760800	Enhancers	NHDF-Ad	bronchial
40	chr2:54758000-54760800	Enhancers	Osteobl	bone
41	chr2:54758000-54761600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:54758000-54762000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:54758000-54762400	Enhancers	HMEC	breast
44	chr2:54758000-54762600	Enhancers	Brain Substantia Nigra	brain
45	chr2:54758200-54760400	Enhancers	Muscle Satellite Cultured Cells	--
46	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
47	chr2:54758400-54760200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:54758600-54760800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:54758600-54761000	Weak transcription	Fetal Heart	heart
50	chr2:54758600-54761200	Enhancers	Brain Angular Gyrus	brain

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