Variant report

Variant	rs4768716
Chromosome Location	chr12:46831158-46831159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46761485..46763714-chr12:46828699..46831336,2	MCF-7	breast:
2	chr12:46763770..46766829-chr12:46827133..46832449,5	MCF-7	breast:
3	chr12:46747388..46749855-chr12:46827679..46831428,3	K562	blood:
4	chr12:46825701..46828001-chr12:46831066..46833593,2	K562	blood:
5	chr12:46760616..46768014-chr12:46824033..46835241,16	K562	blood:
6	chr12:46831045..46834457-chr12:46835919..46840293,4	MCF-7	breast:
7	chr12:46764063..46766992-chr12:46830927..46834019,4	K562	blood:

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10748448	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10748450	0.86[EUR][1000 genomes]
rs10785627	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10785628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10785629	0.86[EUR][1000 genomes]
rs10880947	0.84[MEX][hapmap]
rs10880966	0.83[AMR][1000 genomes]
rs10880967	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10880968	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10880969	0.85[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880970	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880971	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10880973	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11183456	1.00[CHB][hapmap]
rs11183478	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11183479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183483	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11183484	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11183486	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11183488	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11183503	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11183504	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap]
rs11183521	1.00[LWK][hapmap]
rs1125909	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11561535	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11837427	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12099669	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12298616	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12314541	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12319162	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12813763	0.89[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes]
rs12814298	0.88[AMR][1000 genomes]
rs12814341	0.86[AMR][1000 genomes]
rs12822345	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12824565	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12832425	0.86[AMR][1000 genomes]
rs12832777	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472178	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1472179	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1492895	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1667	1.00[LWK][hapmap]
rs2045556	0.86[CHB][hapmap]
rs2131371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2220727	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2252238	0.93[CHD][hapmap];1.00[LWK][hapmap]
rs2408497	0.81[AMR][1000 genomes]
rs2408498	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2897951	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3936214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4072304	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4076247	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4077707	0.95[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs4077708	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs4258438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4427617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768118	0.95[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4768119	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768121	0.90[AMR][1000 genomes]
rs4768122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768123	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4768699	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs4768709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768710	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768711	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4768712	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768713	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768714	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768715	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4768717	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768718	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768719	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs4768724	0.86[EUR][1000 genomes]
rs4768725	0.86[EUR][1000 genomes]
rs4768726	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768727	0.94[MEX][hapmap]
rs4768728	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768729	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768730	0.94[MEX][hapmap]
rs6582636	0.89[JPT][hapmap]
rs6582641	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6582642	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6582643	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6582645	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6582646	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6582657	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6582658	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6582659	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7134289	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7301001	0.90[AMR][1000 genomes]
rs7311504	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7312259	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7316127	0.84[MEX][hapmap]
rs7485580	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7485599	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486495	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7486532	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7486580	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7486596	0.80[EUR][1000 genomes]
rs7487828	0.87[AMR][1000 genomes]
rs7487877	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7488450	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488577	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7489242	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959731	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7968897	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7976280	0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs7980455	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7980775	0.85[MEX][hapmap]
rs9669404	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9706162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9971879	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]

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
rs4768716	LALBA	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46821600-46848600	Weak transcription	Primary B cells from cord blood	blood
2	chr12:46822400-46833600	Enhancers	Hela-S3	cervix
3	chr12:46825400-46844200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:46825600-46843800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:46826400-46832600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:46826400-46832600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:46826400-46836000	Weak transcription	NH-A	brain
8	chr12:46826400-46839200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:46826600-46836400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:46826800-46836000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:46828000-46831800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:46828000-46832600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:46828000-46833600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:46828000-46835800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:46828000-46856000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:46828200-46832600	Weak transcription	NHEK	skin
17	chr12:46828200-46833600	Weak transcription	HMEC	breast
18	chr12:46828800-46831400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:46829000-46832400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:46829200-46831600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:46830400-46831600	Enhancers	A549	lung
22	chr12:46830600-46831200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:46830600-46831200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr12:46830600-46831200	Enhancers	Left Ventricle	heart
25	chr12:46830600-46831200	Enhancers	Ovary	ovary
26	chr12:46830600-46831200	Enhancers	K562	blood
27	chr12:46830600-46834800	Enhancers	HUVEC	blood vessel
28	chr12:46830800-46832000	Weak transcription	Pancreas	Pancrea
29	chr12:46831000-46833600	Weak transcription	NHLF	lung

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