Variant report

Variant	rs62411419
Chromosome Location	chr6:56776472-56776473
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	chr6:56775814..56778593-chr6:56816617..56819922,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151917	Chromatin interaction
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10498814	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12175661	0.91[EUR][1000 genomes]
rs13205191	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16888268	0.92[EUR][1000 genomes]
rs17758527	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17758663	0.92[EUR][1000 genomes]
rs1839837	0.92[EUR][1000 genomes]
rs1903331	0.99[ASN][1000 genomes]
rs2306011	0.92[EUR][1000 genomes]
rs28498151	0.92[EUR][1000 genomes]
rs35942895	1.00[ASN][1000 genomes]
rs4576249	0.91[EUR][1000 genomes]
rs57994994	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58099889	0.92[EUR][1000 genomes]
rs58332182	0.83[EUR][1000 genomes]
rs59106338	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60401134	0.92[EUR][1000 genomes]
rs60910121	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411412	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411417	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411418	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411420	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411421	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411422	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411423	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411425	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62411430	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62417377	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62417378	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62417385	0.90[EUR][1000 genomes]
rs9349842	0.92[EUR][1000 genomes]
rs9357936	0.91[EUR][1000 genomes]
rs9367700	0.92[EUR][1000 genomes]
rs9367701	0.92[EUR][1000 genomes]
rs9367702	0.92[EUR][1000 genomes]
rs9370550	0.92[EUR][1000 genomes]
rs9370553	0.92[EUR][1000 genomes]
rs9370554	0.92[EUR][1000 genomes]
rs9382673	0.92[EUR][1000 genomes]
rs9396238	0.92[EUR][1000 genomes]
rs9396240	0.92[EUR][1000 genomes]
rs9396245	0.92[EUR][1000 genomes]
rs9396251	0.88[EUR][1000 genomes]
rs9396254	0.91[EUR][1000 genomes]
rs9464411	0.92[EUR][1000 genomes]
rs9464412	0.92[EUR][1000 genomes]
rs9464413	0.92[EUR][1000 genomes]
rs9475757	0.92[EUR][1000 genomes]
rs9475761	0.92[EUR][1000 genomes]
rs9475762	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv5315	chr6:56752042-56798761	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56770000-56776800	Weak transcription	Placenta	Placenta
2	chr6:56770000-56779200	Weak transcription	Brain Angular Gyrus	brain
3	chr6:56771600-56777600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:56772000-56777400	Weak transcription	K562	blood
5	chr6:56774000-56779600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:56775400-56778000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:56775600-56777600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr6:56775600-56777600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr6:56775600-56777600	Enhancers	NHEK	skin
10	chr6:56775600-56777800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr6:56775600-56777800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr6:56775600-56778400	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr6:56775600-56778400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr6:56775600-56778400	Enhancers	HSMM	muscle
15	chr6:56775600-56779400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:56775800-56776600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:56775800-56776800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr6:56775800-56777000	Enhancers	A549	lung
19	chr6:56775800-56777200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:56775800-56777600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:56775800-56777600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:56775800-56777800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr6:56775800-56777800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:56775800-56778000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr6:56775800-56779600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:56775800-56780600	Enhancers	NHLF	lung
27	chr6:56775800-56781200	Enhancers	Osteobl	bone
28	chr6:56776000-56777000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:56776000-56777000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:56776000-56777000	Enhancers	Placenta Amnion	Placenta Amnion
31	chr6:56776000-56777400	Enhancers	HMEC	breast
32	chr6:56776000-56777600	Enhancers	H9 Cell Line	embryonic stem cell
33	chr6:56776000-56778200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr6:56776200-56776600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:56776200-56776600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:56776200-56776600	Flanking Active TSS	NH-A	brain
37	chr6:56776200-56776800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:56776200-56777000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr6:56776200-56777000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:56776400-56776600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:56776400-56776600	Flanking Active TSS	HSMMtube	muscle
42	chr6:56776400-56776600	Enhancers	NHDF-Ad	bronchial
43	chr6:56776400-56777600	Weak transcription	Fetal Brain Female	brain
44	chr6:56776400-56778800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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