Variant report

Variant	rs707552
Chromosome Location	chr20:52960053-52960054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52958855..52961034-chr20:53073110..53075206,2	MCF-7	breast:
2	chr20:52884175..52887299-chr20:52959985..52962637,4	MCF-7	breast:
3	chr20:52955260..52957425-chr20:52959176..52960946,2	K562	blood:
4	chr20:52932642..52935057-chr20:52959854..52962762,2	K562	blood:
5	chr20:52955311..52960636-chr20:52963948..52966775,4	MCF-7	breast:
6	chr20:52823411..52827857-chr20:52956007..52962022,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1087050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1293147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16999413	1.00[CEU][hapmap]
rs377448	1.00[CEU][hapmap]
rs6013977	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs6013981	0.93[ASN][1000 genomes]
rs6023041	1.00[CEU][hapmap]
rs6097927	0.87[ASN][1000 genomes]
rs7264904	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs793039	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs793040	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs793045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs793046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs793047	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs793048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs793049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs793050	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs811571	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
3	nsv834012	chr20:52921007-53097177	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs707552	FXYD2	trans	lymphoblastoid	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52956000-52963800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr20:52957400-52961400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr20:52957600-52962000	Weak transcription	Colon Smooth Muscle	Colon
4	chr20:52957800-52960200	Weak transcription	A549	lung
5	chr20:52957800-52960800	Enhancers	HUVEC	blood vessel
6	chr20:52958000-52961200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr20:52958000-52961400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr20:52958000-52961400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr20:52958200-52961200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr20:52958200-52961200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr20:52958200-52961400	Weak transcription	Psoas Muscle	Psoas
12	chr20:52958200-52961400	Weak transcription	NH-A	brain
13	chr20:52958400-52961200	Weak transcription	NHDF-Ad	bronchial
14	chr20:52958400-52961200	Weak transcription	Osteobl	bone
15	chr20:52958400-52961400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr20:52958600-52960200	Weak transcription	Hela-S3	cervix
17	chr20:52958600-52960400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:52959200-52960200	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr20:52959200-52960400	Enhancers	Fetal Brain Male	brain
20	chr20:52959600-52963000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr20:52959800-52961400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr20:52959800-52963600	Weak transcription	Fetal Brain Female	brain
23	chr20:52959800-52964400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr20:52960000-52960200	Enhancers	Brain Germinal Matrix	brain
25	chr20:52960000-52961200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr20:52960000-52961800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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