Variant report

Variant	rs4768719
Chromosome Location	chr12:46840838-46840839
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46765015..46767501-chr12:46840652..46844110,3	MCF-7	breast:
2	chr12:46835538..46838564-chr12:46838793..46843578,4	MCF-7	breast:
3	chr12:46839274..46841469-chr12:46940549..46942826,2	K562	blood:
4	chr12:46835571..46842966-chr12:46847412..46853177,10	MCF-7	breast:
5	chr12:46762033..46769988-chr12:46831671..46842896,19	MCF-7	breast:
6	chr12:46840761..46844133-chr12:46846897..46850857,3	K562	blood:

Variant related genes	Relation type
ENSG00000258096	Chromatin interaction
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10748448	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10748450	0.91[EUR][1000 genomes]
rs10785627	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10785628	0.91[EUR][1000 genomes]
rs10785629	0.91[EUR][1000 genomes]
rs10880967	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10880968	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10880969	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10880970	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10880971	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10880973	0.91[EUR][1000 genomes]
rs11183478	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11183479	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183483	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11183484	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11183486	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11183488	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1125909	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12099669	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12298616	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12314541	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12319162	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12813763	0.82[AMR][1000 genomes]
rs12814298	0.88[AMR][1000 genomes]
rs12814341	0.82[AMR][1000 genomes]
rs12822345	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12824565	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12832425	0.82[AMR][1000 genomes]
rs12832777	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1472178	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1472179	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1492895	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2131371	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2220727	0.93[EUR][1000 genomes]
rs2408498	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2897951	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3936214	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4072304	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4076247	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4077707	0.89[EUR][1000 genomes]
rs4077708	0.91[EUR][1000 genomes]
rs4258438	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4427617	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768118	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4768119	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768121	0.85[AMR][1000 genomes]
rs4768122	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768123	0.90[EUR][1000 genomes]
rs4768709	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768710	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4768711	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4768712	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4768713	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4768714	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4768715	0.86[EUR][1000 genomes]
rs4768716	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768717	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4768718	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4768723	0.91[EUR][1000 genomes]
rs4768724	0.91[EUR][1000 genomes]
rs4768725	0.91[EUR][1000 genomes]
rs6582641	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6582642	0.85[EUR][1000 genomes]
rs6582643	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6582645	0.93[EUR][1000 genomes]
rs6582646	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6582657	0.91[EUR][1000 genomes]
rs6582658	0.91[EUR][1000 genomes]
rs7134289	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7301001	0.85[AMR][1000 genomes]
rs7311504	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7312259	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7485580	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7485599	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7486495	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7486532	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7486580	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7487828	0.83[AMR][1000 genomes]
rs7487877	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7488450	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7489242	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7959731	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7968897	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9669404	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9971879	0.82[AMR][1000 genomes];0.93[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

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46821600-46848600	Weak transcription	Primary B cells from cord blood	blood
2	chr12:46825400-46844200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:46825600-46843800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:46828000-46856000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:46831200-46843200	Weak transcription	Left Ventricle	heart
6	chr12:46834000-46844000	Weak transcription	Esophagus	oesophagus
7	chr12:46834400-46846200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:46836800-46844000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:46836800-46844200	Weak transcription	NH-A	brain
10	chr12:46837000-46841400	Enhancers	NHEK	skin
11	chr12:46837000-46844000	Weak transcription	Fetal Intestine Small	intestine
12	chr12:46837000-46844000	Weak transcription	Osteobl	bone
13	chr12:46837200-46841400	Enhancers	Hela-S3	cervix
14	chr12:46837400-46843200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:46837400-46844000	Weak transcription	Gastric	stomach
16	chr12:46837600-46844000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:46838600-46843200	Weak transcription	K562	blood
18	chr12:46839000-46841200	Enhancers	Fetal Lung	lung
19	chr12:46839200-46843800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:46839200-46844000	Weak transcription	Spleen	Spleen
21	chr12:46839800-46841000	Enhancers	A549	lung
22	chr12:46839800-46841800	Weak transcription	Psoas Muscle	Psoas
23	chr12:46839800-46843600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr12:46839800-46843800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:46839800-46844000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:46839800-46844400	Weak transcription	Small Intestine	intestine
27	chr12:46840000-46841200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr12:46840000-46842800	Weak transcription	Primary T cells from cord blood	blood
29	chr12:46840000-46843400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:46840000-46844000	Weak transcription	Adipose Nuclei	Adipose
31	chr12:46840000-46844200	Weak transcription	Right Ventricle	heart
32	chr12:46840000-46844200	Weak transcription	NHDF-Ad	bronchial
33	chr12:46840600-46841800	Weak transcription	Ovary	ovary
34	chr12:46840600-46843600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:46840600-46843800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:46840600-46843800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:46840600-46843800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:46840800-46841600	Weak transcription	Pancreas	Pancrea
39	chr12:46840800-46841800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:46840800-46841800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:46840800-46841800	Weak transcription	HepG2	liver
42	chr12:46840800-46843000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:46840800-46843000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:46840800-46843000	Weak transcription	Dnd41	blood
45	chr12:46840800-46843200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:46840800-46843200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:46840800-46843200	Weak transcription	Fetal Kidney	kidney
48	chr12:46840800-46843200	Weak transcription	Right Atrium	heart
49	chr12:46840800-46843600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:46840800-46843600	Weak transcription	Primary hematopoietic stem cells	blood

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