Variant report

Variant	rs4241539
Chromosome Location	chr3:20003611-20003612
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:19999505..20001254-chr3:20002139..20004557,2	MCF-7	breast:
2	chr3:20002287..20004974-chr3:20006037..20009711,3	K562	blood:
3	chr3:20002226..20004591-chr3:20006312..20009350,3	MCF-7	breast:
4	chr3:20002484..20004895-chr3:20024210..20026501,2	K562	blood:
5	chr3:19988030..19989664-chr3:20003556..20005607,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10510497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374092	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488378	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12490848	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495866	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497549	1.00[ASN][1000 genomes]
rs17006416	1.00[ASW][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs17006418	0.90[AFR][1000 genomes]
rs17006433	0.90[AFR][1000 genomes]
rs17006435	1.00[ASW][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs17006443	0.84[ASW][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs17180771	0.80[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap]
rs17181337	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17796230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365374	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28597881	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2866630	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3849533	0.80[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap]
rs4398451	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs45542931	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618239	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858116	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858632	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858662	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858664	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858674	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797296	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55892327	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56029370	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56994247	0.90[AFR][1000 genomes]
rs57181336	0.90[AFR][1000 genomes]
rs57382802	0.90[AFR][1000 genomes]
rs59361244	0.90[AFR][1000 genomes]
rs61255313	0.90[AFR][1000 genomes]
rs62241279	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241280	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241285	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62241289	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241295	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241316	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241322	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241326	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241330	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241333	1.00[ASN][1000 genomes]
rs62241334	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241337	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62243065	1.00[ASN][1000 genomes]
rs62243074	1.00[ASN][1000 genomes]
rs62243075	1.00[ASN][1000 genomes]
rs62243076	1.00[ASN][1000 genomes]
rs6802632	0.86[YRI][hapmap]
rs73032477	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034166	1.00[ASN][1000 genomes]
rs9810613	0.80[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap]

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	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4241539	EFHB	cis	parietal	SCAN
rs4241539	RPL15	cis	parietal	SCAN
rs4241539	EFHB	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19989800-20018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:19990000-20008600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:19990000-20016200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:19990800-20017000	Weak transcription	Fetal Kidney	kidney
5	chr3:19991400-20017000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:19991600-20003800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:19991600-20003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:19992000-20004000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:19992200-20012200	Weak transcription	Stomach Mucosa	stomach
10	chr3:19992600-20003800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:19993600-20015600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:19993600-20023600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:19993800-20016200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:19993800-20023800	Weak transcription	Small Intestine	intestine
15	chr3:19994000-20015800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:19994000-20017400	Weak transcription	HSMMtube	muscle
17	chr3:19994600-20011600	Weak transcription	Brain Substantia Nigra	brain
18	chr3:19994600-20013800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:19995600-20017000	Weak transcription	Brain Germinal Matrix	brain
20	chr3:19995800-20016800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:19995800-20021800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:19996400-20003800	Weak transcription	Esophagus	oesophagus
23	chr3:19996400-20017200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:19996400-20021000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:19996600-20007200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:19996600-20015600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:19996600-20016800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:19996800-20007800	Weak transcription	Adipose Nuclei	Adipose
29	chr3:19997200-20013200	Weak transcription	HMEC	breast
30	chr3:19997200-20017000	Weak transcription	HUVEC	blood vessel
31	chr3:19997600-20011800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:19997600-20015200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:19997800-20008400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:19997800-20013200	Weak transcription	NHLF	lung
35	chr3:19997800-20015400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:19997800-20015600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:19997800-20016200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:19997800-20017000	Weak transcription	Brain Anterior Caudate	brain
39	chr3:19997800-20023200	Weak transcription	Spleen	Spleen
40	chr3:19998000-20011800	Weak transcription	Gastric	stomach
41	chr3:19998000-20017000	Weak transcription	HepG2	liver
42	chr3:19998200-20013200	Weak transcription	Osteobl	bone
43	chr3:19998400-20013200	Weak transcription	NHDF-Ad	bronchial
44	chr3:19998800-20004800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:19998800-20011800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:19998800-20013600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:19999000-20003800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:19999000-20007200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:19999000-20011800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:19999000-20013400	Weak transcription	NH-A	brain

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