Variant report

Variant	rs1984651
Chromosome Location	chr7:66281040-66281041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10231411	0.82[TSI][hapmap]
rs10235334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs10235423	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10264223	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10264873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs10267922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10270138	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10275343	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10275956	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10282522	0.82[YRI][hapmap]
rs10479729	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1064795	0.84[TSI][hapmap];0.88[YRI][hapmap]
rs12531365	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12532805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs12534188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs12534948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs12537474	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12538038	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1589887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17680606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs1882657	0.80[TSI][hapmap]
rs2077180	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2091315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs28729561	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3778914	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3778916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs4382352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs4617036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs56743740	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs59765110	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs61554495	0.82[AFR][1000 genomes]
rs62465677	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62465679	0.85[AMR][1000 genomes]
rs62465704	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7777631	0.84[TSI][hapmap]
rs7785755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv981513	chr7:66276464-66291614	Weak transcription Enhancers Strong transcription Genic enhancers	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1984651	GUSB	cis	parietal	SCAN
rs1984651	GUSB	cis	cerebellum	SCAN
rs1984651	TPST1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66261000-66281400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:66275600-66281200	Weak transcription	Right Ventricle	heart
3	chr7:66276000-66282200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:66276000-66282800	Weak transcription	Brain Germinal Matrix	brain
5	chr7:66276200-66282000	Weak transcription	GM12878-XiMat	blood
6	chr7:66276200-66282200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:66276600-66281200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr7:66276800-66281200	Weak transcription	Fetal Thymus	thymus
9	chr7:66276800-66284800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:66277000-66281200	Weak transcription	HMEC	breast
11	chr7:66277000-66282000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:66277000-66282000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr7:66277000-66282200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:66277200-66281200	Weak transcription	NHEK	skin
15	chr7:66277200-66282200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:66277200-66282200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr7:66277400-66281400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:66277800-66284800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:66277800-66288600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr7:66278400-66282000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr7:66278400-66282200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr7:66278400-66282200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr7:66278400-66282200	Weak transcription	HepG2	liver
24	chr7:66278600-66281200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:66278600-66281400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:66278600-66282200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr7:66278600-66282200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr7:66278600-66282200	Weak transcription	Adipose Nuclei	Adipose
29	chr7:66278600-66282200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr7:66278600-66282200	Weak transcription	HSMMtube	muscle
31	chr7:66278800-66282000	Weak transcription	Fetal Intestine Small	intestine
32	chr7:66278800-66284800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr7:66279000-66283400	Weak transcription	Fetal Stomach	stomach
34	chr7:66279400-66281800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:66279800-66281400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr7:66280600-66283200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr7:66281000-66281200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:66281000-66281200	Enhancers	Fetal Muscle Leg	muscle
39	chr7:66281000-66282200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr7:66281000-66282400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr7:66281000-66282400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links