Variant report

Variant	rs151671
Chromosome Location	chr6:80653642-80653643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:80653198..80656160-chr6:80712595..80714599,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112742	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1007416	0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12663071	0.80[ASN][1000 genomes]
rs13191201	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13199685	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201038	0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13207287	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13216035	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1398161	0.83[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1398162	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1398163	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1398164	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512118	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs151666	0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs151667	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs151669	0.99[ASN][1000 genomes]
rs16891260	0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1742475	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2322554	0.83[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs239517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239520	0.83[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs239521	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs239523	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs239524	0.97[ASN][1000 genomes]
rs239526	0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs239527	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs239528	0.97[ASN][1000 genomes]
rs239529	0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs239532	0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2991	0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs343618	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs343620	0.97[ASN][1000 genomes]
rs343623	0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs343627	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs343628	0.83[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs343629	0.83[JPT][hapmap];0.97[ASN][1000 genomes]
rs343632	0.97[ASN][1000 genomes]
rs343693	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs343694	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs343696	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs343697	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs343698	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs343699	0.95[ASN][1000 genomes]
rs343705	0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs35163932	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36067513	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3812153	0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4706819	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6454139	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6928446	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71565059	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7743696	0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7754628	0.83[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754984	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770586	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs865264	0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs9352784	0.86[EUR][1000 genomes]
rs9443725	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9443726	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9448853	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9448857	0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9448858	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9448861	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9448862	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9448863	0.83[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv3475140	chr6:80592690-80679283	Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv3475142	chr6:80592789-80679132	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80618400-80656000	Weak transcription	Aorta	Aorta
2	chr6:80632000-80654800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:80640200-80654800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:80650800-80653800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr6:80651000-80653800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr6:80651000-80655200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr6:80651000-80655600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr6:80652000-80654400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:80652000-80654800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:80652000-80654800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr6:80652000-80655800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:80652000-80656200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:80652200-80655600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
14	chr6:80652800-80653800	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr6:80653000-80653800	Transcr. at gene 5' and 3'	Thymus	Thymus
16	chr6:80653000-80653800	Transcr. at gene 5' and 3'	Dnd41	blood
17	chr6:80653000-80654800	Enhancers	Fetal Brain Female	brain
18	chr6:80653000-80655000	Enhancers	Fetal Brain Male	brain
19	chr6:80653000-80655600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:80653200-80653800	Enhancers	H9 Cell Line	embryonic stem cell
21	chr6:80653200-80654400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:80653200-80655800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:80653400-80654400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr6:80653400-80654400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:80653400-80654400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:80653400-80654400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:80653400-80654600	Weak transcription	HMEC	breast
28	chr6:80653400-80654800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr6:80653600-80654400	Weak transcription	Brain Anterior Caudate	brain
30	chr6:80653600-80654400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:80653600-80654800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:80653600-80654800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:80653600-80655800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:80653600-80656400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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