Variant report

Variant	rs9823770
Chromosome Location	chr3:112990285-112990286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:112990197-112990297	MCF-7	breast:	n/a	n/a
2	CTCF	chr3:112990180-112990330	SAEC	small airway:	n/a	n/a
3	CTCF	chr3:112990188-112990323	MCF-7	breast:	n/a	n/a
4	CTCF	chr3:112990201-112990313	MCF-7	breast:	n/a	n/a
5	CTCF	chr3:112990188-112990313	MCF-7	breast:	n/a	n/a
6	NFIC	chr3:112989978-112990633	ECC-1	luminal epithelium:	n/a	n/a
7	CTCF	chr3:112990225-112990314	NHEK	skin:	n/a	n/a
8	CTCF	chr3:112990260-112990410	BE2_C	brain:	n/a	n/a
9	CTCF	chr3:112990177-112990331	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
BOC	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10511324	0.90[EUR][1000 genomes]
rs13326562	0.81[EUR][1000 genomes]
rs1499898	0.82[YRI][hapmap];0.91[AFR][1000 genomes]
rs16860720	0.82[YRI][hapmap];0.91[AFR][1000 genomes]
rs16860734	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28679287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3995908	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6438134	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6763234	1.00[CEU][hapmap]
rs6780720	1.00[CEU][hapmap]
rs6808103	1.00[CEU][hapmap]
rs7625829	1.00[CEU][hapmap]
rs7629636	1.00[CEU][hapmap]
rs7652801	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9288980	0.90[EUR][1000 genomes]
rs9810059	1.00[CEU][hapmap]
rs9811168	0.81[EUR][1000 genomes]
rs9819129	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9820139	0.83[YRI][hapmap];0.91[AFR][1000 genomes]
rs9820627	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9831049	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831364	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831793	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9832953	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs9836199	0.81[EUR][1000 genomes]
rs9837357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9840485	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9851183	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9852068	1.00[CEU][hapmap]
rs9853439	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9863114	0.81[EUR][1000 genomes]
rs9864630	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9872998	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:112969800-112991800	Weak transcription	Right Ventricle	heart
3	chr3:112969800-112994200	Weak transcription	Spleen	Spleen
4	chr3:112973600-112993000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
6	chr3:112974200-112994600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:112978600-112991400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:112981200-112991000	Genic enhancers	Fetal Muscle Leg	muscle
9	chr3:112981600-112994400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:112982800-112993600	Weak transcription	HMEC	breast
11	chr3:112983800-112995000	Weak transcription	Lung	lung
12	chr3:112984000-112994400	Weak transcription	HSMMtube	muscle
13	chr3:112984200-112993600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:112984200-112994400	Weak transcription	HSMM	muscle
15	chr3:112984600-112991200	Weak transcription	Brain Germinal Matrix	brain
16	chr3:112984600-112993400	Weak transcription	Fetal Brain Male	brain
17	chr3:112984800-112992400	Weak transcription	Fetal Thymus	thymus
18	chr3:112984800-112993000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:112984800-112998400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:112985400-112993600	Strong transcription	Fetal Lung	lung
22	chr3:112986200-112990400	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr3:112986200-112994200	Strong transcription	Ovary	ovary
24	chr3:112986400-112993000	Strong transcription	Fetal Intestine Small	intestine
25	chr3:112986400-112994600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:112986600-112990600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:112986600-112993800	Weak transcription	Brain Substantia Nigra	brain
28	chr3:112987200-112990600	Strong transcription	Fetal Intestine Large	intestine
29	chr3:112987200-112993400	Strong transcription	Fetal Stomach	stomach
30	chr3:112987200-112994400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:112987400-112991200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:112987800-112991200	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:112987800-112996000	Enhancers	Pancreas	Pancrea
34	chr3:112988000-112991000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:112988000-112992200	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:112988000-112993600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:112988000-112993800	Weak transcription	Brain Angular Gyrus	brain
38	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr3:112988200-112992600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:112988200-112993400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:112988200-112993600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:112988200-112993800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:112988200-112994200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:112988200-112994200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:112988200-112994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:112988400-112991600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:112988400-112994000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:112988400-112994600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr3:112988400-112996800	Weak transcription	Placenta	Placenta
50	chr3:112989000-112990400	Genic enhancers	Colon Smooth Muscle	Colon

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