Variant report

Variant	rs9870654
Chromosome Location	chr3:99788463-99788464
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99603110..99605515-chr3:99787025..99789865,2	MCF-7	breast:
2	chr3:99787349..99788508-chr3:99972741..99973631,4	MCF-7	breast:
3	chr3:99787292..99788466-chr3:99972325..99973638,6	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12330859	1.00[AFR][1000 genomes]
rs13326499	0.83[AFR][1000 genomes]
rs16841897	0.83[AFR][1000 genomes]
rs16841922	1.00[AFR][1000 genomes]
rs9820656	0.83[AFR][1000 genomes]
rs9826443	0.83[AFR][1000 genomes]
rs9830284	0.83[AFR][1000 genomes]
rs9837440	0.83[AFR][1000 genomes]
rs9841296	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]
rs9871820	1.00[AFR][1000 genomes]
rs9883757	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:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99767600-99801000	Weak transcription	HSMM	muscle
2	chr3:99774000-99794800	Weak transcription	Stomach Mucosa	stomach
3	chr3:99783200-99792400	Weak transcription	Psoas Muscle	Psoas
4	chr3:99783200-99793600	Weak transcription	Aorta	Aorta
5	chr3:99783400-99791400	Enhancers	HepG2	liver
6	chr3:99783600-99788600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:99783600-99791200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:99783600-99792200	Weak transcription	Fetal Lung	lung
9	chr3:99784200-99791400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:99784200-99792400	Weak transcription	Fetal Stomach	stomach
11	chr3:99784400-99789400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:99786800-99790400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:99786800-99790400	Weak transcription	Small Intestine	intestine
14	chr3:99787000-99792200	Weak transcription	Fetal Intestine Small	intestine
15	chr3:99787600-99795200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:99787800-99788600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr3:99787800-99788600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:99787800-99788600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr3:99787800-99788600	Enhancers	Brain Substantia Nigra	brain
20	chr3:99787800-99788800	Enhancers	Primary B cells from peripheral blood	blood
21	chr3:99787800-99788800	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr3:99787800-99789000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:99787800-99789000	Enhancers	HUVEC	blood vessel
24	chr3:99787800-99789200	Enhancers	Primary hematopoietic stem cells	blood
25	chr3:99787800-99792200	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr3:99787800-99792600	Enhancers	Osteobl	bone
27	chr3:99788000-99788800	Enhancers	Brain Hippocampus Middle	brain
28	chr3:99788000-99789000	ZNF genes & repeats	Primary B cells from cord blood	blood
29	chr3:99788000-99789000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr3:99788000-99790000	Weak transcription	K562	blood
31	chr3:99788000-99790200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:99788000-99790600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:99788000-99791000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:99788000-99792200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:99788000-99792800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:99788200-99788600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:99788200-99788600	Enhancers	Colon Smooth Muscle	Colon
38	chr3:99788200-99789600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:99788200-99790200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:99788200-99790200	Weak transcription	Placenta	Placenta
41	chr3:99788200-99790200	Weak transcription	NHLF	lung
42	chr3:99788200-99790400	Weak transcription	GM12878-XiMat	blood
43	chr3:99788200-99791000	Weak transcription	Fetal Heart	heart
44	chr3:99788200-99791400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:99788200-99791600	Weak transcription	Fetal Intestine Large	intestine
46	chr3:99788200-99791800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:99788200-99792000	Weak transcription	Fetal Thymus	thymus
48	chr3:99788200-99792200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:99788200-99792600	Weak transcription	Thymus	Thymus
50	chr3:99788400-99789200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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