Variant report

Variant	rs6442050
Chromosome Location	chr3:47013730-47013731
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	chr3:47007836..47011318-chr3:47011441..47014509,4	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11130109	0.81[AFR][1000 genomes]
rs11706212	0.84[AFR][1000 genomes]
rs11709876	0.86[AFR][1000 genomes]
rs11715389	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13062185	0.85[AFR][1000 genomes]
rs13062516	0.82[AFR][1000 genomes]
rs13082531	0.84[AFR][1000 genomes]
rs1463394	0.81[AFR][1000 genomes]
rs2124510	0.87[AFR][1000 genomes]
rs2385868	0.86[AFR][1000 genomes]
rs2891892	0.83[AFR][1000 genomes]
rs2891893	0.81[AFR][1000 genomes]
rs4324490	0.86[AFR][1000 genomes]
rs4378998	0.86[AFR][1000 genomes]
rs4389512	0.86[AFR][1000 genomes]
rs4408896	1.00[ASN][1000 genomes]
rs4435675	0.83[AFR][1000 genomes]
rs4435676	0.88[AFR][1000 genomes]
rs4522803	0.80[AFR][1000 genomes]
rs4543047	0.86[AFR][1000 genomes]
rs4682835	0.81[AFR][1000 genomes]
rs4682836	0.81[AFR][1000 genomes]
rs4683285	0.80[AFR][1000 genomes]
rs6442044	0.81[AFR][1000 genomes]
rs6442047	0.86[AFR][1000 genomes]
rs6442048	0.87[AFR][1000 genomes]
rs6766676	0.81[AFR][1000 genomes]
rs6806521	0.86[AFR][1000 genomes]
rs7624549	0.81[AFR][1000 genomes]
rs7625011	0.88[AFR][1000 genomes]
rs7646076	0.80[AFR][1000 genomes]
rs7649941	0.81[AFR][1000 genomes]
rs936181	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1012682	chr3:46973552-47016357	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
9	esv1800172	chr3:47013346-47049306	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47003200-47015800	Weak transcription	Fetal Brain Male	brain
2	chr3:47003200-47016800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:47004800-47017200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:47004800-47017200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:47006600-47014400	Genic enhancers	Fetal Thymus	thymus
6	chr3:47006600-47017000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:47006800-47014600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:47007000-47017400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:47007200-47013800	Enhancers	Fetal Heart	heart
10	chr3:47007200-47017400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:47007400-47013800	Strong transcription	Fetal Stomach	stomach
12	chr3:47007600-47013800	Enhancers	Pancreas	Pancrea
13	chr3:47007600-47014600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr3:47007600-47014800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:47007600-47016200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:47007600-47017200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:47007600-47017200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:47007600-47017400	Weak transcription	HSMMtube	muscle
19	chr3:47008200-47014600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr3:47008400-47015600	Weak transcription	Hela-S3	cervix
21	chr3:47009200-47017200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:47009400-47014800	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr3:47010200-47014400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:47010200-47014400	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr3:47010400-47013800	Genic enhancers	Fetal Muscle Leg	muscle
26	chr3:47010400-47014200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr3:47010600-47015400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:47011200-47014600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr3:47011200-47015600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:47011200-47017200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:47011200-47017200	Weak transcription	Aorta	Aorta
32	chr3:47011400-47013800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:47011400-47016200	Weak transcription	HMEC	breast
34	chr3:47011600-47013800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:47011800-47013800	Enhancers	HUVEC	blood vessel
36	chr3:47011800-47014000	Enhancers	Psoas Muscle	Psoas
37	chr3:47012000-47013800	Enhancers	Small Intestine	intestine
38	chr3:47012000-47014600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:47012200-47015800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr3:47012400-47014200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:47012600-47014600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:47012600-47016000	Enhancers	Primary B cells from peripheral blood	blood
43	chr3:47012800-47013800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:47012800-47014200	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr3:47012800-47015800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:47012800-47017200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr3:47013000-47013800	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr3:47013000-47013800	Enhancers	Spleen	Spleen
49	chr3:47013000-47014200	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:47013000-47015600	Weak transcription	Colonic Mucosa	Colon

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