Variant report

Variant	rs4687608
Chromosome Location	chr3:52097060-52097061
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	chr3:52088485..52093169-chr3:52093699..52100396,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf74-1	chr3:52096110-52099128	NONHSAT089896

Variant related genes	Relation type
ENSG00000164086	Chromatin interaction

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

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

rs_ID	r²[population]
rs12485855	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12488456	0.83[EUR][1000 genomes]
rs12489539	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12493204	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs17051963	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3821841	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs4687609	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4687798	0.86[MEX][hapmap]
rs4687801	0.85[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4687802	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4687806	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4687809	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs72622937	0.87[AFR][1000 genomes]
rs7618573	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs920160	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs9873175	0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
9	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	esv1797189	chr3:52070955-52101799	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	esv1798365	chr3:52070955-52101799	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv590282	chr3:52088204-52097060	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv1836489	chr3:52089837-52101799	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	esv1838771	chr3:52089837-52101799	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv590293	chr3:52089889-52097060	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52091800-52101800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:52091800-52106000	Enhancers	Esophagus	oesophagus
3	chr3:52092000-52097600	Enhancers	GM12878-XiMat	blood
4	chr3:52092000-52099200	Weak transcription	Right Atrium	heart
5	chr3:52092000-52102200	Enhancers	HMEC	breast
6	chr3:52092000-52106400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr3:52092200-52099200	Weak transcription	Gastric	stomach
8	chr3:52092200-52101400	Weak transcription	Fetal Intestine Large	intestine
9	chr3:52092200-52102800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:52092200-52102800	Weak transcription	Thymus	Thymus
11	chr3:52092200-52104200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:52092200-52104800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:52092200-52107800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:52092600-52104800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:52094000-52102000	Enhancers	NHEK	skin
16	chr3:52094200-52098800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:52094600-52097200	Enhancers	Stomach Mucosa	stomach
18	chr3:52094800-52097400	Enhancers	Placenta Amnion	Placenta Amnion
19	chr3:52094800-52097800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr3:52095000-52097400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:52095200-52097800	Enhancers	Placenta	Placenta
22	chr3:52095400-52097200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:52095600-52097800	Enhancers	Primary B cells from peripheral blood	blood
24	chr3:52095800-52097200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:52095800-52097800	Enhancers	Fetal Muscle Leg	muscle
26	chr3:52096000-52099200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:52096000-52107800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:52096200-52097400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:52096200-52097600	Enhancers	Brain Hippocampus Middle	brain
30	chr3:52096200-52099600	Enhancers	Fetal Muscle Trunk	muscle
31	chr3:52096200-52102000	Enhancers	Fetal Stomach	stomach
32	chr3:52096400-52097200	Enhancers	HUVEC	blood vessel
33	chr3:52096400-52097200	Enhancers	NH-A	brain
34	chr3:52096400-52097200	Enhancers	Osteobl	bone
35	chr3:52096400-52097400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:52096400-52097400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:52096400-52097400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:52096400-52097400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr3:52096400-52097400	Enhancers	HSMM	muscle
40	chr3:52096400-52097400	Enhancers	NHDF-Ad	bronchial
41	chr3:52096400-52097600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:52096400-52097600	Enhancers	HSMMtube	muscle
43	chr3:52096400-52097600	Enhancers	NHLF	lung
44	chr3:52096400-52106400	Weak transcription	Fetal Thymus	thymus
45	chr3:52096600-52097200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:52096600-52097400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr3:52096600-52097600	Enhancers	Brain Anterior Caudate	brain
48	chr3:52096600-52097600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr3:52096600-52097600	Enhancers	Brain Substantia Nigra	brain
50	chr3:52096600-52099400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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