Variant report

Variant	rs62406498
Chromosome Location	chr6:36917189-36917190
allele	C/T
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	ESR1	chr6:36917019-36917419	ECC-1	luminal epithelium:	n/a	chr6:36917192-36917207
2	ESR1	chr6:36917061-36917345	ECC-1	luminal epithelium:	n/a	chr6:36917192-36917207
3	ESR1	chr6:36916990-36917343	ECC-1	luminal epithelium:	n/a	chr6:36917192-36917207
4	ESR1	chr6:36916958-36917376	ECC-1	luminal epithelium:	n/a	chr6:36917192-36917207
5	MYC	chr6:36917009-36917209	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:36915747..36919680-chr6:36919787..36923449,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTCH1-1	chr6:36917155-36917266	ucscGeneNc_uc003omt_1

Variant related genes	Relation type
ENSG00000232598	TF binding region
ENSG00000164530	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17624006	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272194	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272198	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58012316	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406491	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406492	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406493	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406499	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406518	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406522	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs708005	0.89[EUR][1000 genomes]
rs708006	0.81[EUR][1000 genomes]
rs72846863	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72846873	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72848004	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470445	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv519499	chr6:36915906-36924102	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv522653	chr6:36915906-36925774	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36898600-36922200	Weak transcription	Right Atrium	heart
2	chr6:36914400-36917200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr6:36915400-36917800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:36915400-36918000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:36915600-36917200	Weak transcription	NHEK	skin
6	chr6:36915800-36918000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr6:36916000-36917200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:36916000-36917200	Enhancers	Hela-S3	cervix
9	chr6:36916000-36917200	Weak transcription	NH-A	brain
10	chr6:36916000-36921400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:36916000-36923000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:36916200-36917200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:36916200-36917200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:36916200-36917200	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:36916200-36917200	Weak transcription	HMEC	breast
16	chr6:36916200-36917600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:36916200-36919400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:36916200-36920800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr6:36916200-36920800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:36916200-36921200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr6:36916200-36921200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr6:36916200-36921600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:36916200-36922600	Weak transcription	Brain Anterior Caudate	brain
24	chr6:36916200-36923000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:36916400-36917400	Enhancers	Fetal Thymus	thymus
26	chr6:36916400-36917600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:36916400-36920600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:36916400-36920600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:36916400-36920600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:36916400-36921400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:36916400-36921400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:36916400-36921400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr6:36916600-36920600	Weak transcription	Primary B cells from cord blood	blood
34	chr6:36916600-36921200	Weak transcription	Primary T cells from cord blood	blood
35	chr6:36916600-36921800	Weak transcription	Dnd41	blood
36	chr6:36916800-36918600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:36916800-36921200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr6:36917000-36917200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:36917000-36917200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr6:36917000-36917400	Enhancers	HUVEC	blood vessel
41	chr6:36917000-36917600	Enhancers	Brain Cingulate Gyrus	brain
42	chr6:36917000-36917800	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr6:36917000-36917800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:36917000-36918000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:36917000-36918000	Enhancers	Brain Substantia Nigra	brain
46	chr6:36917000-36918000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr6:36917000-36918200	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr6:36917000-36918200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr6:36917000-36918200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:36917000-36921000	Weak transcription	Primary B cells from peripheral blood	blood

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