Variant report

Variant	rs62407578
Chromosome Location	chr6:28954712-28954713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28952766..28954746-chr6:28971481..28973784,3	MCF-7	breast:
2	chr6:28891456..28893478-chr6:28954362..28956726,2	K562	blood:
3	chr6:28948241..28954799-chr6:28970209..28976187,12	MCF-7	breast:
4	chr6:28889368..28892748-chr6:28952347..28956108,5	MCF-7	breast:
5	chr6:28804483..28808288-chr6:28953262..28955503,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf100-3	chr6:28954454-28955261	ENSG00000227214.2

Variant related genes	Relation type
ENSG00000204713	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000197935	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10484544	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12663679	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12663717	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12665108	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs16894533	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16894540	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894554	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2269554	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28796930	0.81[EUR][1000 genomes]
rs3116845	0.85[EUR][1000 genomes]
rs3130719	0.86[EUR][1000 genomes]
rs56080800	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56131223	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57232568	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57332439	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58065505	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58836159	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58912940	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61554786	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62407581	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62407603	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62407619	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
3	nsv1023540	chr6:28922691-29326018	Active TSS Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538169	chr6:28922691-29326018	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv869541	chr6:28922692-29326017	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv916439	chr6:28922697-29326087	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv462668	chr6:28922719-29342775	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv601213	chr6:28922719-29342775	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv1015796	chr6:28923980-29342825	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv462669	chr6:28936556-29337500	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv601214	chr6:28936556-29337500	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv601215	chr6:28946920-29348297	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28948600-28954800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:28951000-28955800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:28951000-28956000	Weak transcription	GM12878-XiMat	blood
4	chr6:28953400-28955800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr6:28953800-28956400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:28954000-28954800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:28954000-28955200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:28954000-28955800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:28954000-28955800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:28954000-28956000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:28954000-28956000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:28954000-28956000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:28954000-28956000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:28954000-28956000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:28954000-28956000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr6:28954000-28956000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:28954000-28956000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:28954000-28956000	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:28954000-28956000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:28954000-28956000	Weak transcription	Psoas Muscle	Psoas
21	chr6:28954000-28956000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:28954000-28956000	Weak transcription	HSMM	muscle
23	chr6:28954000-28956000	Weak transcription	HUVEC	blood vessel
24	chr6:28954000-28956000	Weak transcription	NH-A	brain
25	chr6:28954000-28956000	Weak transcription	NHLF	lung
26	chr6:28954000-28956200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:28954000-28956200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:28954000-28956200	Weak transcription	Esophagus	oesophagus
29	chr6:28954000-28956200	Weak transcription	Gastric	stomach
30	chr6:28954000-28956200	Weak transcription	Right Atrium	heart
31	chr6:28954000-28956200	Weak transcription	HSMMtube	muscle
32	chr6:28954000-28956200	Weak transcription	NHDF-Ad	bronchial
33	chr6:28954200-28956000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr6:28954200-28956000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr6:28954200-28956000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr6:28954200-28956000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:28954200-28956000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:28954200-28956000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:28954200-28956000	Weak transcription	Adipose Nuclei	Adipose
40	chr6:28954200-28956000	Weak transcription	Fetal Kidney	kidney
41	chr6:28954200-28956000	Weak transcription	Right Ventricle	heart
42	chr6:28954200-28956000	Weak transcription	NHEK	skin
43	chr6:28954200-28956000	Weak transcription	Osteobl	bone
44	chr6:28954200-28956200	Weak transcription	Brain Anterior Caudate	brain
45	chr6:28954200-28956200	Weak transcription	Ovary	ovary
46	chr6:28954200-28956200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:28954200-28956200	Weak transcription	Spleen	Spleen
48	chr6:28954400-28954800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr6:28954400-28955800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr6:28954400-28956000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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