Variant report

Variant	rs1992375
Chromosome Location	chr8:49837844-49837845
allele	A/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	RAD21	chr8:49837649-49837971	SK-N-SH_RA	brain:	n/a	n/a
2	RAD21	chr8:49837442-49839138	SK-N-SH	brain:	n/a	chr8:49838357-49838366 chr8:49838348-49838367
3	RAD21	chr8:49837829-49838736	MCF-7	breast:	n/a	chr8:49838357-49838366 chr8:49838348-49838367
4	CTCF	chr8:49837700-49837850	AG09319	gingival:	n/a	n/a
5	GATA3	chr8:49837743-49838608	MCF-7	breast:	n/a	chr8:49837843-49837853
6	CTCF	chr8:49837760-49837910	HCFaa	heart:	n/a	n/a
7	CTCF	chr8:49837800-49837950	NHEK	skin:	n/a	n/a
8	RAD21	chr8:49837826-49838791	HCT-116	colon:	n/a	chr8:49838357-49838366 chr8:49838348-49838367
9	GATA3	chr8:49837816-49838756	SK-N-SH	brain:	n/a	chr8:49837843-49837853
10	CTCF	chr8:49837820-49837970	HMF	breast:	n/a	n/a
11	CTCF	chr8:49837517-49839064	A549	lung:	n/a	chr8:49838357-49838364 chr8:49838351-49838367 chr8:49838350-49838368 chr8:49838352-49838365 chr8:49838345-49838366
12	GATA3	chr8:49837725-49838741	T-47D	breast:	n/a	chr8:49837843-49837853
13	CTCF	chr8:49837681-49839012	HCT-116	colon:	n/a	chr8:49838357-49838364 chr8:49838351-49838367 chr8:49838350-49838368 chr8:49838352-49838365 chr8:49838345-49838366
14	RAD21	chr8:49837809-49838735	Hela-S3	cervix:	n/a	chr8:49838357-49838366 chr8:49838348-49838367
15	CTCF	chr8:49837455-49838982	SK-N-SH	brain:	n/a	chr8:49838357-49838364 chr8:49838351-49838367 chr8:49838350-49838368 chr8:49838352-49838365 chr8:49838345-49838366
16	RAD21	chr8:49837624-49838758	IMR90	lung:	n/a	chr8:49838357-49838366 chr8:49838348-49838367
17	CTCF	chr8:49837708-49838669	IMR90	lung:	n/a	chr8:49838357-49838364 chr8:49838351-49838367 chr8:49838350-49838368 chr8:49838352-49838365 chr8:49838345-49838366
18	SMC3	chr8:49837668-49838859	Hela-S3	cervix:	n/a	chr8:49838352-49838366
19	SMC3	chr8:49837533-49839089	SK-N-SH	brain:	n/a	chr8:49838352-49838366

No.	Distal block	Cell Line	Cell type
1	chr8:49236947..49237860-chr8:49837763..49838543,2	MCF-7	breast:
2	chr8:49231028..49232049-chr8:49837754..49838644,8	MCF-7	breast:
3	chr8:49084388..49085321-chr8:49837765..49838724,3	MCF-7	breast:
4	chr8:49178987..49179896-chr8:49837365..49838730,6	MCF-7	breast:
5	chr8:49837099..49839896-chr8:49842697..49845711,3	K562	blood:
6	chr8:49227294..49228250-chr8:49837799..49838312,2	MCF-7	breast:
7	chr8:49668073..49669071-chr8:49837841..49838748,4	MCF-7	breast:
8	chr8:49235083..49235906-chr8:49837806..49838740,2	MCF-7	breast:

Variant related genes	Relation type
SNAI2	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10097264	0.84[EUR][1000 genomes]
rs10100077	0.84[EUR][1000 genomes]
rs11515036	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12682003	0.83[AMR][1000 genomes]
rs13265564	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1441004	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1441005	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17641604	0.85[AMR][1000 genomes]
rs1837690	0.81[AMR][1000 genomes]
rs2385117	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2385120	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2582778	0.85[CEU][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs870397	0.83[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890854	chr8:49738821-49838908	Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:49835000-49838000	Enhancers	Fetal Muscle Leg	muscle
2	chr8:49835000-49838200	Enhancers	Fetal Stomach	stomach
3	chr8:49835000-49840200	Enhancers	Placenta Amnion	Placenta Amnion
4	chr8:49835200-49838200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr8:49835400-49838000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr8:49835400-49838000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr8:49835600-49838000	Weak transcription	Fetal Kidney	kidney
8	chr8:49835800-49838800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr8:49835800-49838800	Enhancers	HMEC	breast
10	chr8:49835800-49839000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr8:49836000-49838800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr8:49836200-49838200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr8:49836200-49838200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr8:49836200-49839200	Enhancers	Fetal Lung	lung
15	chr8:49836400-49838800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr8:49836600-49838800	Enhancers	Hela-S3	cervix
17	chr8:49836800-49838200	Enhancers	HSMMtube	muscle
18	chr8:49836800-49838800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr8:49836800-49838800	Enhancers	NHEK	skin
20	chr8:49836800-49839000	Enhancers	Dnd41	blood
21	chr8:49836800-49843200	Weak transcription	Esophagus	oesophagus
22	chr8:49837000-49838200	Enhancers	HSMM	muscle
23	chr8:49837400-49838000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr8:49837600-49838200	Enhancers	Fetal Brain Male	brain
25	chr8:49837600-49838200	Enhancers	NHDF-Ad	bronchial
26	chr8:49837600-49838200	Enhancers	NHLF	lung
27	chr8:49837600-49838600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr8:49837800-49838000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr8:49837800-49838000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr8:49837800-49838000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr8:49837800-49838000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr8:49837800-49838000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr8:49837800-49838000	Enhancers	Brain Germinal Matrix	brain
34	chr8:49837800-49838600	Enhancers	HUVEC	blood vessel
35	chr8:49837800-49838600	Enhancers	Osteobl	bone
36	chr8:49837800-49839000	Enhancers	NH-A	brain
37	chr8:49837800-49839200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr8:49837800-49846200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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