Variant report

Variant	rs4845719
Chromosome Location	chr1:151933360-151933361
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151919533..151922319-chr1:151932817..151935606,2	MCF-7	breast:
2	chr1:151925413..151928425-chr1:151930738..151934740,3	MCF-7	breast:
3	chr1:151932606..151935514-chr1:151936511..151938848,2	MCF-7	breast:
4	chr1:151913842..151916280-chr1:151933238..151936084,3	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10494270	0.81[AMR][1000 genomes]
rs11204919	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204920	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11582739	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12083193	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12095483	0.85[ASN][1000 genomes]
rs16833668	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16833669	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16833670	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16833728	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16833743	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1844543	0.81[AMR][1000 genomes]
rs2337685	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2337686	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28415528	0.85[EUR][1000 genomes]
rs2932580	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34251437	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3791153	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56000812	0.84[AMR][1000 genomes]
rs56078223	0.84[AMR][1000 genomes]
rs56313205	0.81[AMR][1000 genomes]
rs57785325	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61814883	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61817719	0.81[AMR][1000 genomes]
rs61817720	0.81[AMR][1000 genomes]
rs61817722	0.86[ASN][1000 genomes]
rs61817723	0.84[ASN][1000 genomes]
rs61817724	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61817725	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6587632	0.81[AMR][1000 genomes]
rs6587633	0.81[AMR][1000 genomes]
rs6587634	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6587635	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6587636	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6587637	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6587638	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6587640	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6657658	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6662602	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6662611	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6662728	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6663064	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6675930	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6678672	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6682605	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6684114	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6684312	0.81[AMR][1000 genomes]
rs6686874	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6690449	0.81[AMR][1000 genomes]
rs6691212	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6693388	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6693396	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6693901	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6695324	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6701374	0.84[AMR][1000 genomes]
rs6703448	0.81[AMR][1000 genomes]
rs6703465	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72694840	0.81[AMR][1000 genomes]
rs7535002	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7538652	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7541099	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7554832	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7554859	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs902313	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs971887	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9943221	0.84[AMR][1000 genomes]
rs9943251	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4845719	NBPF18P	cis	Nerve Tibial	GTEx
rs4845719	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs4845719	THEM4	cis	multi-tissue	Pritchard
rs4845719	THEM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151930800-151940800	Weak transcription	NHDF-Ad	bronchial
2	chr1:151931600-151934000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:151931800-151935200	Weak transcription	Hela-S3	cervix
4	chr1:151932800-151933400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:151932800-151934200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:151932800-151934200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:151932800-151934200	Enhancers	Stomach Mucosa	stomach
8	chr1:151932800-151936400	Enhancers	Fetal Kidney	kidney
9	chr1:151933000-151933400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr1:151933000-151933600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr1:151933000-151934000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:151933000-151934200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:151933000-151934200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:151933000-151934400	Enhancers	Fetal Lung	lung
15	chr1:151933000-151934800	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr1:151933000-151934800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr1:151933200-151933400	Enhancers	Adipose Nuclei	Adipose
18	chr1:151933200-151933600	Weak transcription	Fetal Intestine Small	intestine
19	chr1:151933200-151933600	Flanking Active TSS	HUVEC	blood vessel
20	chr1:151933200-151936200	Weak transcription	Monocytes-CD14+_RO01746	blood

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