Variant report

Variant	rs2708588
Chromosome Location	chr7:112030495-112030496
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:112029526..112032512-chr7:112089416..112091655,2	K562	blood:
2	chr7:112029372..112031621-chr7:112036798..112039526,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10238141	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs10272126	0.89[GIH][hapmap];1.00[MEX][hapmap]
rs10272188	0.89[GIH][hapmap]
rs10272976	0.85[CHD][hapmap]
rs10953708	0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10953710	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs11763356	0.87[ASN][1000 genomes]
rs11763588	1.00[ASW][hapmap];0.95[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11763768	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11768608	0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11769219	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.87[ASN][1000 genomes]
rs11770767	0.88[JPT][hapmap]
rs11773393	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12666911	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12673259	1.00[CEU][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13230061	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16873374	0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs17159389	0.89[GIH][hapmap]
rs1985929	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2188534	0.81[CHD][hapmap]
rs2301725	0.81[TSI][hapmap]
rs2520471	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2520473	0.88[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2520475	0.85[MEX][hapmap]
rs2520476	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2523029	1.00[ASN][1000 genomes]
rs2523030	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523035	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523037	0.93[ASN][1000 genomes]
rs2523038	0.93[ASN][1000 genomes]
rs2523039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2523041	0.93[ASN][1000 genomes]
rs2708590	1.00[ASN][1000 genomes]
rs2708592	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708594	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708595	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2708597	0.88[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708598	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708603	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708604	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2708605	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3109114	0.81[GIH][hapmap]
rs34171150	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3807884	0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs3823515	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41281063	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4730516	1.00[JPT][hapmap]
rs55662318	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56969420	0.90[ASN][1000 genomes]
rs6955231	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6978927	0.95[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs735150	0.88[JPT][hapmap]
rs7781245	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs7795336	1.00[JPT][hapmap]
rs9641480	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532335	chr7:111411990-112054905	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
3	nsv1020212	chr7:111944370-112032596	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv831097	chr7:112000837-112113173	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2708588	C7orf53	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112024000-112030600	Weak transcription	Dnd41	blood
2	chr7:112024200-112031400	Weak transcription	Pancreas	Pancrea
3	chr7:112025400-112031400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:112027000-112032000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr7:112027200-112031000	Weak transcription	Fetal Kidney	kidney
6	chr7:112027400-112030800	Weak transcription	Fetal Intestine Large	intestine
7	chr7:112027400-112030800	Weak transcription	Fetal Intestine Small	intestine
8	chr7:112027600-112030600	Weak transcription	Psoas Muscle	Psoas

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