Variant report

Variant	rs9871820
Chromosome Location	chr3:99783198-99783199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99781468..99783579-chr3:99820252..99822252,2	MCF-7	breast:
2	chr3:99770192..99771868-chr3:99780463..99783303,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12330859	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs13326499	0.83[AFR][1000 genomes]
rs1387648	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs16841824	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs16841897	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes]
rs16841922	1.00[AFR][1000 genomes]
rs4434174	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs9819861	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs9820656	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes]
rs9825938	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs9826443	0.83[AFR][1000 genomes]
rs9829693	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs9830284	0.83[AFR][1000 genomes]
rs9837440	0.83[AFR][1000 genomes]
rs9841296	1.00[ASW][hapmap];0.83[AFR][1000 genomes]
rs9841678	0.83[AFR][1000 genomes]
rs9843812	0.83[AFR][1000 genomes]
rs9860687	0.83[AFR][1000 genomes]
rs9861168	1.00[AFR][1000 genomes]
rs9862384	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs9870654	1.00[AFR][1000 genomes]
rs9883757	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];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	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99767600-99801000	Weak transcription	HSMM	muscle
3	chr3:99768400-99788000	Weak transcription	Primary B cells from cord blood	blood
4	chr3:99770800-99787600	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:99774000-99794800	Weak transcription	Stomach Mucosa	stomach
6	chr3:99775000-99785800	Weak transcription	Fetal Intestine Small	intestine
7	chr3:99777400-99787800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:99778600-99784000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:99778600-99787800	Weak transcription	Right Atrium	heart
10	chr3:99780600-99786000	Weak transcription	Fetal Intestine Large	intestine
11	chr3:99782600-99783200	Enhancers	Aorta	Aorta
12	chr3:99782600-99783600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:99782600-99783600	Enhancers	Colon Smooth Muscle	Colon
14	chr3:99782600-99783600	Enhancers	Fetal Lung	lung
15	chr3:99782800-99783200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:99782800-99783200	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr3:99782800-99783200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:99782800-99783200	Enhancers	Psoas Muscle	Psoas
19	chr3:99782800-99783200	Flanking Active TSS	Osteobl	bone
20	chr3:99782800-99783400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:99782800-99783400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:99782800-99783600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:99782800-99783600	Enhancers	Rectal Smooth Muscle	rectum
24	chr3:99782800-99783600	Enhancers	NHDF-Ad	bronchial
25	chr3:99782800-99784200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:99782800-99784200	Enhancers	Fetal Stomach	stomach
27	chr3:99783000-99783200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr3:99783000-99783200	Enhancers	HepG2	liver
29	chr3:99783000-99783600	Enhancers	Ovary	ovary
30	chr3:99783000-99784200	Enhancers	NHLF	lung
31	chr3:99783000-99785800	Weak transcription	Small Intestine	intestine
32	chr3:99783000-99787600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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