Variant report

Variant	rs7757668
Chromosome Location	chr6:1575666-1575667
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXC1-4	chr6:1575444-1575941	NONHSAT106523

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs57459957	1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs57713879	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61437110	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7757665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9501737	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9501738	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9501739	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9501740	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9502966	0.89[ASN][1000 genomes]
rs9502967	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9502970	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9502971	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1024111	chr6:1231850-1730146	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1021924	chr6:1254891-1736995	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv538082	chr6:1254891-1736995	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv917248	chr6:1365437-1627813	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1034039	chr6:1427061-1691837	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv538088	chr6:1427061-1691837	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
8	nsv1027393	chr6:1446300-1692019	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv538089	chr6:1446300-1692019	Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv1016859	chr6:1460020-1645819	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv883376	chr6:1535043-1635082	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv883377	chr6:1552705-1583600	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1573200-1576200	Enhancers	Esophagus	oesophagus
2	chr6:1573400-1576600	Enhancers	GM12878-XiMat	blood
3	chr6:1573600-1576000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:1573600-1576200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr6:1574000-1575800	Enhancers	Fetal Stomach	stomach
6	chr6:1574000-1576000	Enhancers	Fetal Thymus	thymus
7	chr6:1574000-1576200	Enhancers	Brain Anterior Caudate	brain
8	chr6:1574000-1576600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr6:1574000-1576800	Enhancers	Brain Angular Gyrus	brain
10	chr6:1574000-1577000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr6:1574200-1575800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:1574200-1575800	Enhancers	Brain Substantia Nigra	brain
13	chr6:1574200-1576200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:1574200-1576600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr6:1574200-1576600	Enhancers	Fetal Brain Male	brain
16	chr6:1574200-1576800	Enhancers	Fetal Muscle Leg	muscle
17	chr6:1574200-1577200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr6:1574400-1575800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr6:1574400-1576000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:1574400-1576000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:1574400-1576200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:1574400-1576200	Enhancers	Brain Germinal Matrix	brain
23	chr6:1574400-1576400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr6:1574400-1576600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr6:1574400-1576600	Enhancers	Right Ventricle	heart
26	chr6:1574400-1577000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:1574400-1577000	Enhancers	Brain Cingulate Gyrus	brain
28	chr6:1574600-1575800	Enhancers	Brain Hippocampus Middle	brain
29	chr6:1574600-1576000	Enhancers	Dnd41	blood
30	chr6:1574600-1576600	Enhancers	Fetal Lung	lung
31	chr6:1574600-1576800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:1574600-1577200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:1574800-1576200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:1574800-1576400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
35	chr6:1574800-1576600	Enhancers	Placenta	Placenta
36	chr6:1575000-1575800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:1575000-1576200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:1575000-1576400	Enhancers	HSMMtube	muscle
39	chr6:1575200-1575800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr6:1575200-1576200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:1575200-1576200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr6:1575200-1576400	Enhancers	HMEC	breast
43	chr6:1575200-1576600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:1575200-1576600	Enhancers	NHLF	lung
45	chr6:1575400-1575800	Enhancers	Ovary	ovary
46	chr6:1575400-1575800	Enhancers	Right Atrium	heart
47	chr6:1575400-1576000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:1575400-1576000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
49	chr6:1575400-1576000	Flanking Active TSS	HSMM	muscle
50	chr6:1575400-1576200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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