Variant report

Variant	rs6684912
Chromosome Location	chr1:186652175-186652176
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	GATA3	chr1:186651770-186652410	SK-N-SH	brain:	n/a	chr1:186652235-186652256 chr1:186652116-186652129
2	CTCF	chr1:186651893-186652322	MCF-7	breast:	n/a	chr1:186652059-186652080 chr1:186652064-186652082 chr1:186652066-186652079
3	RAD21	chr1:186651691-186652378	SK-N-SH	brain:	n/a	chr1:186652062-186652081
4	CTCF	chr1:186651913-186652260	MCF-7	breast:	n/a	chr1:186652059-186652080 chr1:186652064-186652082 chr1:186652066-186652079
5	RAD21	chr1:186651860-186652212	ECC-1	luminal epithelium:	n/a	chr1:186652062-186652081
6	CTCF	chr1:186651971-186652220	A549	lung:	n/a	chr1:186652059-186652080 chr1:186652064-186652082 chr1:186652066-186652079
7	RAD21	chr1:186651953-186652337	MCF-7	breast:	n/a	chr1:186652062-186652081
8	RFX5	chr1:186651005-186652278	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr1:186651955-186652218	HUVEC	blood vessel:	n/a	chr1:186652059-186652080 chr1:186652064-186652082 chr1:186652066-186652079
10	RAD21	chr1:186651908-186652185	H1-hESC	embryonic stem cell:	n/a	chr1:186652062-186652081
11	GATA3	chr1:186651929-186652368	SK-N-SH	brain:	n/a	chr1:186652235-186652256 chr1:186652116-186652129
12	RAD21	chr1:186651911-186652247	H1-hESC	embryonic stem cell:	n/a	chr1:186652062-186652081
13	CTCF	chr1:186651802-186652366	HCT-116	colon:	n/a	chr1:186652059-186652080 chr1:186652064-186652082 chr1:186652066-186652079
14	RAD21	chr1:186651914-186652218	GM12878	blood:	n/a	chr1:186652062-186652081
15	RAD21	chr1:186651918-186652246	SK-N-SH_RA	brain:	n/a	chr1:186652062-186652081
16	CTCF	chr1:186651906-186652187	A549	lung:	n/a	chr1:186652059-186652080 chr1:186652064-186652082 chr1:186652066-186652079
17	RAD21	chr1:186651731-186652312	A549	lung:	n/a	chr1:186652062-186652081
18	SMC3	chr1:186651670-186652257	Hela-S3	cervix:	n/a	chr1:186652066-186652080
19	TBP	chr1:186648845-186652253	Hela-S3	cervix:	n/a	n/a
20	RAD21	chr1:186651656-186652277	IMR90	lung:	n/a	chr1:186652062-186652081
21	CTCF	chr1:186651997-186652190	Medullo	brain:	n/a	chr1:186652059-186652080 chr1:186652064-186652082 chr1:186652066-186652079
22	RAD21	chr1:186651921-186652229	A549	lung:	n/a	chr1:186652062-186652081
23	CTCF	chr1:186652040-186652190	Caco-2	colon:	n/a	chr1:186652059-186652080 chr1:186652064-186652082 chr1:186652066-186652079
24	CTCF	chr1:186651954-186652237	GM12878	blood:	n/a	chr1:186652059-186652080 chr1:186652064-186652082 chr1:186652066-186652079
25	CTCF	chr1:186651898-186652273	A549	lung:	n/a	chr1:186652059-186652080 chr1:186652064-186652082 chr1:186652066-186652079
26	CTCF	chr1:186651893-186652265	IMR90	lung:	n/a	chr1:186652059-186652080 chr1:186652064-186652082 chr1:186652066-186652079
27	RAD21	chr1:186651832-186652253	Hela-S3	cervix:	n/a	chr1:186652062-186652081
28	RAD21	chr1:186651799-186652357	HCT-116	colon:	n/a	chr1:186652062-186652081
29	CEBPB	chr1:186651856-186652176	Hela-S3	cervix:	n/a	n/a
30	RAD21	chr1:186651891-186652180	H1-hESC	embryonic stem cell:	n/a	chr1:186652062-186652081
31	CTCF	chr1:186651701-186652449	SK-N-SH	brain:	n/a	chr1:186652059-186652080 chr1:186652064-186652082 chr1:186652066-186652079
32	RAD21	chr1:186651874-186652248	SK-N-SH_RA	brain:	n/a	chr1:186652062-186652081
33	RAD21	chr1:186651776-186652356	MCF-7	breast:	n/a	chr1:186652062-186652081
34	RAD21	chr1:186651641-186652287	A549	lung:	n/a	chr1:186652062-186652081
35	RAD21	chr1:186651795-186652360	HCT-116	colon:	n/a	chr1:186652062-186652081
36	SMC3	chr1:186652004-186652204	GM12878	blood:	n/a	chr1:186652066-186652080

No.	Distal block	Cell Line	Cell type
1	chr1:186574544..186575451-chr1:186651610..186652900,9	MCF-7	breast:
2	chr1:186651918..186653014-chr1:186954800..186955506,3	MCF-7	breast:
3	chr1:186451542..186452284-chr1:186651474..186652178,3	MCF-7	breast:
4	chr1:186651621..186652400-chr1:186954720..186955299,2	MCF-7	breast:
5	chr1:186451532..186452512-chr1:186651563..186652631,6	MCF-7	breast:

Variant related genes	Relation type
PTGS2	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16825778	0.84[AFR][1000 genomes]
rs57881663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59356684	0.84[AFR][1000 genomes]
rs6681646	0.80[AFR][1000 genomes]
rs6695769	0.85[AFR][1000 genomes]
rs74134743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74134774	0.80[AFR][1000 genomes]
rs7526535	0.82[AFR][1000 genomes]
rs7556245	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv470750	chr1:186642429-186700959	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv548403	chr1:186642429-186700959	Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186648600-186652400	Active TSS	NHEK	skin
2	chr1:186649200-186652400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:186650200-186652200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:186650600-186652200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr1:186651000-186652600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:186651000-186653200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:186651200-186652800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr1:186651600-186657000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:186651800-186653000	Enhancers	NHLF	lung
10	chr1:186651800-186653400	Enhancers	Hela-S3	cervix
11	chr1:186652000-186652200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:186652000-186652200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:186652000-186652200	Enhancers	HUVEC	blood vessel
14	chr1:186652000-186652600	Enhancers	Rectal Smooth Muscle	rectum
15	chr1:186652000-186652600	Enhancers	A549	lung
16	chr1:186652000-186652600	Enhancers	NHDF-Ad	bronchial
17	chr1:186652000-186653000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:186652000-186653000	Enhancers	Colon Smooth Muscle	Colon
19	chr1:186652000-186653200	Enhancers	Osteobl	bone

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