Variant report

Variant	rs6800456
Chromosome Location	chr3:99617753-99617754
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99586883..99589677-chr3:99616438..99618388,2	K562	blood:
2	chr3:99595513..99598055-chr3:99616729..99618510,2	K562	blood:
3	chr3:99616272..99618855-chr3:99619104..99622005,3	MCF-7	breast:
4	chr3:99593363..99597253-chr3:99616411..99618781,5	K562	blood:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1038295	0.87[ASN][1000 genomes]
rs10804762	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs12486901	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489030	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491153	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12493124	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12493320	1.00[CEU][hapmap]
rs1492343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1565341	0.88[JPT][hapmap]
rs1610263	0.82[CEU][hapmap]
rs1610265	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs1871847	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971381	0.88[JPT][hapmap]
rs35590972	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732444	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3921767	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4408901	0.85[JPT][hapmap]
rs4928143	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4928144	0.88[JPT][hapmap]
rs4928219	1.00[JPT][hapmap]
rs4928220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs4928222	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4928233	0.88[JPT][hapmap];0.93[YRI][hapmap]
rs4928236	0.88[JPT][hapmap];0.85[YRI][hapmap]
rs55874130	0.93[EUR][1000 genomes]
rs55881709	0.89[EUR][1000 genomes]
rs55964918	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56140081	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56223679	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56260910	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56335268	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60119031	0.90[ASN][1000 genomes]
rs61010376	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440991	0.88[JPT][hapmap]
rs6777622	0.85[JPT][hapmap]
rs6778589	0.88[JPT][hapmap]
rs6792339	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73858966	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73859911	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73860464	0.83[ASN][1000 genomes]
rs73860470	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7431827	0.88[JPT][hapmap]
rs7610759	0.88[JPT][hapmap]
rs7614366	0.88[JPT][hapmap]
rs7632327	0.88[JPT][hapmap]
rs7632345	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634628	1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7635633	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7635871	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824430	0.88[JPT][hapmap]
rs9827744	0.88[JPT][hapmap];0.81[YRI][hapmap]
rs9872339	0.88[JPT][hapmap]

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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99600800-99638600	Weak transcription	Left Ventricle	heart
2	chr3:99604600-99648200	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99614800-99619400	Weak transcription	Psoas Muscle	Psoas
4	chr3:99615000-99619400	Weak transcription	Fetal Lung	lung
5	chr3:99615200-99619400	Weak transcription	Brain Angular Gyrus	brain
6	chr3:99615200-99620600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:99615400-99618400	Weak transcription	Adipose Nuclei	Adipose
8	chr3:99615400-99618600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:99615400-99619600	Weak transcription	Stomach Mucosa	stomach
10	chr3:99615400-99619600	Weak transcription	HSMMtube	muscle
11	chr3:99615400-99619800	Weak transcription	Fetal Stomach	stomach
12	chr3:99615400-99619800	Enhancers	NHDF-Ad	bronchial
13	chr3:99615400-99620200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:99615600-99617800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:99615600-99619200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:99615600-99619400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:99615600-99619400	Weak transcription	A549	lung
18	chr3:99615600-99619600	Weak transcription	HSMM	muscle
19	chr3:99615600-99619800	Weak transcription	GM12878-XiMat	blood
20	chr3:99615800-99617800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:99615800-99618400	Weak transcription	NHEK	skin
22	chr3:99615800-99618600	Weak transcription	Hela-S3	cervix
23	chr3:99615800-99619400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:99615800-99619400	Weak transcription	NH-A	brain
25	chr3:99615800-99619400	Weak transcription	Osteobl	bone
26	chr3:99615800-99619600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:99615800-99619800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:99615800-99619800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr3:99616000-99618600	Weak transcription	HMEC	breast
30	chr3:99616000-99619200	Weak transcription	HUVEC	blood vessel
31	chr3:99616000-99619600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:99616000-99620200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:99616000-99620400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:99616000-99631200	Weak transcription	Primary B cells from cord blood	blood
35	chr3:99616200-99619400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:99616200-99619400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:99616200-99619400	Weak transcription	Brain Germinal Matrix	brain
38	chr3:99616200-99619600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:99616400-99619200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr3:99616400-99619200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr3:99616600-99618600	Weak transcription	HepG2	liver
42	chr3:99616600-99619600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:99616600-99622800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:99617000-99618200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:99617000-99618800	Enhancers	NHLF	lung
46	chr3:99617200-99623200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:99617400-99617800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:99617600-99619600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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