Variant report

Variant	rs9860687
Chromosome Location	chr3:99742046-99742047
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99741282..99743622-chr3:99746551..99748156,2	MCF-7	breast:
2	chr3:99741319..99743139-chr3:99748165..99750114,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12330859	0.83[AFR][1000 genomes]
rs13326499	1.00[AFR][1000 genomes]
rs16841897	1.00[AFR][1000 genomes]
rs16841922	0.83[AFR][1000 genomes]
rs9820656	1.00[AFR][1000 genomes]
rs9826443	1.00[AFR][1000 genomes]
rs9830284	1.00[AFR][1000 genomes]
rs9837440	1.00[AFR][1000 genomes]
rs9841296	1.00[AFR][1000 genomes]
rs9841678	1.00[AFR][1000 genomes]
rs9843812	1.00[AFR][1000 genomes]
rs9861168	0.83[AFR][1000 genomes]
rs9870654	0.83[AFR][1000 genomes]
rs9871820	0.83[AFR][1000 genomes]
rs9883757	1.00[AFR][1000 genomes]
rs9990322	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99716400-99758800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:99722400-99751000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:99725000-99745600	Weak transcription	Left Ventricle	heart
5	chr3:99725200-99743600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:99726400-99748200	Weak transcription	HSMM	muscle
7	chr3:99727000-99746400	Weak transcription	Right Atrium	heart
8	chr3:99728400-99760400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr3:99728800-99746200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:99733800-99745800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:99735600-99750400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:99738400-99744400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:99739200-99743800	Enhancers	Adipose Nuclei	Adipose
14	chr3:99739800-99742400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr3:99739800-99744800	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr3:99740600-99743200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:99740800-99743000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:99741000-99744200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:99741000-99744200	Enhancers	Pancreas	Pancrea
20	chr3:99741000-99744800	Enhancers	Psoas Muscle	Psoas
21	chr3:99741200-99743400	Enhancers	NHEK	skin
22	chr3:99741200-99743800	Enhancers	HMEC	breast
23	chr3:99741200-99744400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:99741200-99744600	Enhancers	NH-A	brain
25	chr3:99741200-99744600	Enhancers	Osteobl	bone
26	chr3:99741200-99766800	Weak transcription	Right Ventricle	heart
27	chr3:99741400-99742400	Enhancers	Aorta	Aorta
28	chr3:99741400-99744400	Enhancers	HepG2	liver
29	chr3:99741400-99744800	Enhancers	NHDF-Ad	bronchial
30	chr3:99741600-99742200	Enhancers	Brain Cingulate Gyrus	brain
31	chr3:99741600-99742200	Enhancers	Placenta Amnion	Placenta Amnion
32	chr3:99741600-99742600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:99741600-99743000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:99741600-99744200	Enhancers	Small Intestine	intestine
35	chr3:99741600-99744400	Enhancers	Fetal Intestine Large	intestine
36	chr3:99741600-99744800	Enhancers	Ovary	ovary
37	chr3:99741800-99742200	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr3:99741800-99742600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:99741800-99742800	Enhancers	Fetal Brain Male	brain
40	chr3:99741800-99743200	Enhancers	Brain Hippocampus Middle	brain
41	chr3:99741800-99744200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:99741800-99744200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:99741800-99744200	Enhancers	Esophagus	oesophagus
44	chr3:99741800-99744600	Enhancers	Fetal Intestine Small	intestine
45	chr3:99741800-99745200	Enhancers	Stomach Mucosa	stomach
46	chr3:99742000-99742200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr3:99742000-99742200	Enhancers	Gastric	stomach
48	chr3:99742000-99742200	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr3:99742000-99742400	Enhancers	NHLF	lung
50	chr3:99742000-99742600	Enhancers	Cortex derived primary cultured neurospheres	brain

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