Variant report

Variant	rs9860986
Chromosome Location	chr3:99617026-99617027
allele	A/G
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	chr3:99614799..99617137-chr3:99982145..99984761,3	K562	blood:
4	chr3:99616272..99618855-chr3:99619104..99622005,3	MCF-7	breast:
5	chr3:99593363..99597253-chr3:99616411..99618781,5	K562	blood:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12330310	1.00[AFR][1000 genomes]
rs13315221	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs13320602	1.00[YRI][hapmap]
rs13323384	1.00[AFR][1000 genomes]
rs13327351	0.83[AFR][1000 genomes]
rs13353487	1.00[AFR][1000 genomes]
rs16841800	1.00[AFR][1000 genomes]
rs16841824	1.00[AFR][1000 genomes]
rs16841828	0.83[AFR][1000 genomes]
rs16841836	1.00[AFR][1000 genomes]
rs16846956	0.83[AFR][1000 genomes]
rs28368726	1.00[AFR][1000 genomes]
rs28411225	0.83[AFR][1000 genomes]
rs28463921	1.00[AFR][1000 genomes]
rs28508384	1.00[AFR][1000 genomes]
rs28728176	0.83[AFR][1000 genomes]
rs28816814	1.00[AFR][1000 genomes]
rs9809706	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9810553	1.00[AFR][1000 genomes]
rs9816232	1.00[AFR][1000 genomes]
rs9816617	1.00[YRI][hapmap]
rs9820799	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9824229	1.00[AFR][1000 genomes]
rs9825382	1.00[AFR][1000 genomes]
rs9825938	1.00[AFR][1000 genomes]
rs9828782	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9830038	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9830284	1.00[YRI][hapmap]
rs9831309	1.00[YRI][hapmap]
rs9831706	0.83[AFR][1000 genomes]
rs9833005	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9835048	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9837028	1.00[AFR][1000 genomes]
rs9837204	1.00[AFR][1000 genomes]
rs9837555	1.00[AFR][1000 genomes]
rs9841053	1.00[AFR][1000 genomes]
rs9841758	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9843919	1.00[AFR][1000 genomes]
rs9844578	1.00[AFR][1000 genomes]
rs9844595	1.00[AFR][1000 genomes]
rs9849336	1.00[AFR][1000 genomes]
rs9849373	1.00[AFR][1000 genomes]
rs9851406	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9851985	0.83[AFR][1000 genomes]
rs9852857	1.00[AFR][1000 genomes]
rs9862370	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9868303	1.00[AFR][1000 genomes]
rs9870153	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9871500	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9875301	1.00[AFR][1000 genomes]
rs9883235	1.00[YRI][hapmap];1.00[AFR][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	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	chr3:99615600-99617600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:99615600-99617800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:99615600-99619200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:99615600-99619400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:99615600-99619400	Weak transcription	A549	lung
19	chr3:99615600-99619600	Weak transcription	HSMM	muscle
20	chr3:99615600-99619800	Weak transcription	GM12878-XiMat	blood
21	chr3:99615800-99617800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:99615800-99618400	Weak transcription	NHEK	skin
23	chr3:99615800-99618600	Weak transcription	Hela-S3	cervix
24	chr3:99615800-99619400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:99615800-99619400	Weak transcription	NH-A	brain
26	chr3:99615800-99619400	Weak transcription	Osteobl	bone
27	chr3:99615800-99619600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:99615800-99619800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:99615800-99619800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:99616000-99617200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:99616000-99618600	Weak transcription	HMEC	breast
32	chr3:99616000-99619200	Weak transcription	HUVEC	blood vessel
33	chr3:99616000-99619600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:99616000-99620200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:99616000-99620400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:99616000-99631200	Weak transcription	Primary B cells from cord blood	blood
37	chr3:99616200-99619400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:99616200-99619400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:99616200-99619400	Weak transcription	Brain Germinal Matrix	brain
40	chr3:99616200-99619600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:99616400-99617200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:99616400-99619200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr3:99616400-99619200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr3:99616600-99618600	Weak transcription	HepG2	liver
45	chr3:99616600-99619600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:99616600-99622800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:99617000-99618200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:99617000-99618800	Enhancers	NHLF	lung

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