Variant report

Variant	rs2668566
Chromosome Location	chr4:54522240-54522241
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	CTCF	chr4:54522160-54522310	NHDF-neo	bronchial:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54480528..54481474-chr4:54522217..54523059,3	MCF-7	breast:

Variant related genes	Relation type
LNX1	TF binding region
ENSG00000249341	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1079230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1107027	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477875	0.89[ASN][1000 genomes]
rs1477876	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1546526	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972815	0.89[CEU][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1996005	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164266	0.91[ASN][1000 genomes]
rs2572283	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2572291	0.89[ASN][1000 genomes]
rs2572299	0.89[ASN][1000 genomes]
rs2590780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2590781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2590816	0.88[CEU][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2590823	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2616386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2616410	0.81[EUR][1000 genomes]
rs2668516	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2668521	0.89[ASN][1000 genomes]
rs2668524	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668529	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668548	0.91[EUR][1000 genomes]
rs2668549	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668557	0.87[EUR][1000 genomes]
rs7686480	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs907510	0.81[EUR][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	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54515600-54522400	Enhancers	Stomach Mucosa	stomach
2	chr4:54517600-54523200	Weak transcription	Spleen	Spleen
3	chr4:54518000-54523200	Weak transcription	HSMM	muscle
4	chr4:54519400-54523600	Enhancers	Fetal Muscle Leg	muscle
5	chr4:54519600-54522400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:54519600-54522400	Enhancers	NHDF-Ad	bronchial
7	chr4:54519600-54522800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:54519600-54522800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:54519600-54523400	Enhancers	NHLF	lung
10	chr4:54519800-54522400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:54520200-54524400	Weak transcription	Ovary	ovary
12	chr4:54520800-54524000	Weak transcription	Fetal Heart	heart
13	chr4:54521000-54524200	Weak transcription	Fetal Stomach	stomach
14	chr4:54521200-54522400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:54521200-54522400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:54521600-54522800	Weak transcription	Osteobl	bone
17	chr4:54521600-54523400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:54521800-54522800	Weak transcription	NHEK	skin
19	chr4:54522000-54522400	Enhancers	Duodenum Mucosa	Duodenum
20	chr4:54522000-54524600	Weak transcription	Colon Smooth Muscle	Colon
21	chr4:54522200-54522400	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr4:54522200-54522800	Weak transcription	Esophagus	oesophagus
23	chr4:54522200-54526000	Weak transcription	Gastric	stomach
24	chr4:54522200-54526000	Weak transcription	Right Atrium	heart

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