Variant report

Variant	rs4768727
Chromosome Location	chr12:46864205-46864206
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46862072..46864676-chr12:46865439..46867529,2	K562	blood:
2	chr12:46862072..46864676-chr12:46865439..46867529,3	K562	blood:
3	chr12:46763940..46766014-chr12:46863555..46865794,3	K562	blood:
4	chr12:46765375..46766918-chr12:46861342..46864304,2	MCF-7	breast:
5	chr12:46857414..46859341-chr12:46861249..46864836,4	K562	blood:

Variant related genes	Relation type
ENSG00000258096	Chromatin interaction
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10748448	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10748450	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10785628	0.85[AMR][1000 genomes]
rs10785629	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10880973	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10880974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183478	0.94[MEX][hapmap]
rs11183483	0.94[MEX][hapmap]
rs11183486	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11183502	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11183503	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11183504	1.00[CEU][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11837427	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12313929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12314541	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12321960	0.95[YRI][hapmap]
rs12813763	0.84[MEX][hapmap]
rs12824565	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap]
rs12827740	0.83[AMR][1000 genomes]
rs2131371	0.94[MEX][hapmap]
rs2252238	0.95[CEU][hapmap]
rs3925101	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3935048	0.97[LWK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs4077707	0.85[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4077708	0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs4768118	0.80[CHB][hapmap];0.84[CHD][hapmap];0.94[MEX][hapmap]
rs4768123	0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs4768699	0.90[JPT][hapmap]
rs4768716	0.94[MEX][hapmap]
rs4768723	0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs4768724	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4768725	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4768726	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768728	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768729	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768730	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768733	0.95[CEU][hapmap]
rs6582645	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6582657	0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6582658	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6582659	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6582660	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486915	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488577	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7953339	1.00[YRI][hapmap]
rs7954645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7959731	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap]
rs7960808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7980455	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9669404	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap]
rs9706162	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9706460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9706520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9971879	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap]

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	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4768727	LALBA	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46844600-46866000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:46844600-46886000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:46853200-46867400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:46854800-46866000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:46856000-46864800	Weak transcription	Small Intestine	intestine
6	chr12:46856000-46867800	Weak transcription	Aorta	Aorta
7	chr12:46856200-46866000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:46856200-46866200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:46856200-46868200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:46856600-46867400	Weak transcription	Placenta	Placenta
11	chr12:46857800-46864800	Weak transcription	Ovary	ovary
12	chr12:46858800-46867400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:46860000-46866000	Weak transcription	K562	blood
14	chr12:46860000-46866200	Weak transcription	Fetal Intestine Small	intestine
15	chr12:46860200-46867400	Enhancers	Hela-S3	cervix
16	chr12:46860800-46866800	Enhancers	HUVEC	blood vessel
17	chr12:46861200-46867000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:46861400-46866600	Enhancers	A549	lung
19	chr12:46861600-46864800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:46861600-46864800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:46862200-46864800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:46862200-46864800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:46862400-46864800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:46862400-46864800	Weak transcription	NHEK	skin
25	chr12:46862600-46864800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:46862600-46864800	Weak transcription	Stomach Mucosa	stomach
27	chr12:46862600-46865200	Weak transcription	NH-A	brain
28	chr12:46863200-46867400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:46863400-46864400	Enhancers	Primary B cells from cord blood	blood
30	chr12:46863400-46864400	Enhancers	Primary B cells from peripheral blood	blood
31	chr12:46863400-46864400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr12:46863400-46864400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr12:46863400-46865000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:46863400-46867400	Enhancers	Primary hematopoietic stem cells	blood
35	chr12:46863600-46864400	Enhancers	Primary T cells from cord blood	blood
36	chr12:46863600-46864400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:46863600-46864400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:46863600-46864400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr12:46863600-46864400	Flanking Active TSS	Dnd41	blood
40	chr12:46863600-46865400	Enhancers	Fetal Heart	heart
41	chr12:46863800-46864400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr12:46863800-46864400	Enhancers	Primary T cells fromperipheralblood	blood
43	chr12:46863800-46864400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr12:46863800-46864400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:46863800-46864400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:46863800-46864400	Enhancers	Fetal Thymus	thymus
47	chr12:46863800-46864400	Flanking Active TSS	GM12878-XiMat	blood
48	chr12:46863800-46865000	Enhancers	Left Ventricle	heart
49	chr12:46863800-46865400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr12:46863800-46866600	Enhancers	HepG2	liver

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