Variant report

Variant	rs62413365
Chromosome Location	chr6:80248336-80248337
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr6:80246302-80248785	H1-neurons	neurons:	n/a	n/a
2	MXI1	chr6:80245777-80249441	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr6:80245862-80249600	MCF10A-Er-Src	breast:	n/a	n/a
4	YY1	chr6:80248042-80248626	SK-N-SH_RA	brain:	n/a	chr6:80248212-80248220
5	POLR2A	chr6:80247928-80248771	H1-neurons	neurons:	n/a	n/a
6	FOS	chr6:80248198-80248539	MCF10A-Er-Src	breast:	n/a	n/a
7	ARID3A	chr6:80246977-80248592	K562	blood:	n/a	n/a
8	IRF1	chr6:80246841-80248706	K562	blood:	n/a	chr6:80247824-80247834 chr6:80246916-80246930 chr6:80247820-80247834
9	FOS	chr6:80247101-80248812	MCF10A-Er-Src	breast:	n/a	chr6:80247333-80247347 chr6:80247193-80247202 chr6:80247511-80247520
10	IRF1	chr6:80245900-80248704	K562	blood:	n/a	chr6:80247824-80247834 chr6:80246916-80246930 chr6:80246283-80246297 chr6:80246281-80246292 chr6:80247820-80247834 chr6:80246279-80246293
11	POLR2A	chr6:80246567-80248715	H1-neurons	neurons:	n/a	n/a
12	ZNF384	chr6:80246806-80248632	K562	blood:	n/a	n/a
13	MAFK	chr6:80247254-80248611	K562	blood:	n/a	chr6:80247575-80247590
14	RFX5	chr6:80245421-80249050	SK-N-SH	brain:	n/a	chr6:80248388-80248397 chr6:80247194-80247203
15	POLR2A	chr6:80246317-80249494	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr6:80246134-80248476	IMR90	lung:	n/a	n/a
17	FOS	chr6:80246984-80248415	HUVEC	blood vessel:	n/a	chr6:80247333-80247347 chr6:80247193-80247202 chr6:80247511-80247520
18	FOS	chr6:80247301-80248568	MCF10A-Er-Src	breast:	n/a	chr6:80247333-80247347 chr6:80247511-80247520
19	TBP	chr6:80246187-80248519	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:79786363..79788558-chr6:80246704..80249654,3	K562	blood:
2	chr6:80247904..80250067-chr6:80253206..80255779,2	MCF-7	breast:
3	chr6:79784764..79788097-chr6:80246158..80249987,4	MCF-7	breast:
4	chr6:79786974..79789353-chr6:80246033..80249654,3	K562	blood:

Variant related genes	Relation type
LCA5	TF binding region
ENSG00000146247	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12178357	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs16890740	1.00[AFR][1000 genomes]
rs16890789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16890805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16890832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2134854	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62411327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62411328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62411329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62411333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62411355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62411357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411359	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413369	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413383	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62413386	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62413394	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62413400	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62413402	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62413403	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62413404	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62413406	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62413407	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62413408	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62413409	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62413411	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62413412	0.90[AMR][1000 genomes]
rs62413418	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62413420	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62413423	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv830707	chr6:80134625-80325171	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1029259	chr6:80142754-80340332	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv886303	chr6:80147225-80252423	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv463906	chr6:80240951-80313297	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv604052	chr6:80240951-80313297	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1018318	chr6:80241029-80465282	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80243000-80249400	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr6:80245000-80248800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:80245000-80249200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr6:80245200-80248800	Active TSS	Fetal Brain Male	brain
5	chr6:80245400-80249400	Active TSS	Right Atrium	heart
6	chr6:80245600-80248400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:80245600-80248800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:80245600-80248800	Active TSS	NHLF	lung
9	chr6:80245600-80249400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr6:80245800-80248400	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr6:80245800-80248400	Active TSS	Osteobl	bone
12	chr6:80245800-80248600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:80245800-80248800	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr6:80245800-80249400	Active TSS	K562	blood
15	chr6:80245800-80249600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:80246000-80248400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr6:80246000-80248400	Active TSS	H1 Cell Line	embryonic stem cell
18	chr6:80246000-80248400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:80246000-80248400	Active TSS	Fetal Muscle Leg	muscle
20	chr6:80246000-80248400	Active TSS	NHDF-Ad	bronchial
21	chr6:80246000-80248600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:80246000-80248600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:80246000-80248600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:80246000-80248600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:80246000-80248600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:80246000-80248600	Active TSS	Brain Substantia Nigra	brain
27	chr6:80246000-80248600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr6:80246000-80248600	Active TSS	Fetal Intestine Large	intestine
29	chr6:80246000-80248600	Active TSS	Fetal Lung	lung
30	chr6:80246000-80248600	Active TSS	Fetal Stomach	stomach
31	chr6:80246000-80248600	Active TSS	Ovary	ovary
32	chr6:80246000-80248600	Active TSS	HSMM	muscle
33	chr6:80246000-80248600	Active TSS	HSMMtube	muscle
34	chr6:80246000-80248800	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr6:80246000-80248800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:80246000-80248800	Active TSS	Aorta	Aorta
37	chr6:80246000-80248800	Active TSS	Duodenum Mucosa	Duodenum
38	chr6:80246000-80248800	Active TSS	Psoas Muscle	Psoas
39	chr6:80246000-80248800	Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr6:80246000-80248800	Active TSS	Stomach Smooth Muscle	stomach
41	chr6:80246000-80249000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:80246000-80249400	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr6:80246000-80249600	Active TSS	Brain Angular Gyrus	brain
44	chr6:80246200-80248400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:80246200-80248400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:80246200-80248400	Active TSS	Placenta Amnion	Placenta Amnion
47	chr6:80246200-80248400	Active TSS	Rectal Smooth Muscle	rectum
48	chr6:80246200-80248400	Active TSS	NH-A	brain
49	chr6:80246200-80248600	Active TSS	Colon Smooth Muscle	Colon
50	chr6:80246200-80248600	Active TSS	Duodenum Smooth Muscle	Duodenum

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