Variant report

Variant	rs1204556
Chromosome Location	chr7:126584795-126584796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:126584558-126585048..7:126890676-126899918	H1-hESC	embryonic stem cell:	embryo
2	chr7:126577088..126579543-chr7:126581963..126584921,2	K562	blood:

Variant related genes	Relation type
ENSG00000179603	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1003037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1003038	1.00[CEU][hapmap]
rs10239010	1.00[CHB][hapmap]
rs1154326	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1154333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs1155655	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1155657	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1204554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1204555	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204557	1.00[CEU][hapmap]
rs1204558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1204559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204560	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1204561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1204562	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1204565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1204566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs1204568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1204570	1.00[JPT][hapmap]
rs1204572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs1204573	1.00[CEU][hapmap]
rs1204574	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204582	1.00[JPT][hapmap]
rs1204585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs1204589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1204590	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap]
rs1204595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1361970	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1419455	0.85[EUR][1000 genomes]
rs1419456	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1419457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1419463	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs1419466	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17864092	1.00[JPT][hapmap]
rs2021162	1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2109740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2254259	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254260	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518946	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2518948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2518952	0.92[EUR][1000 genomes]
rs2518956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2535928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2535937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2896388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs916614	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529300	chr7:125669493-126587858	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1032938	chr7:126067684-126587859	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv539119	chr7:126067684-126587859	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2758132	chr7:126494789-126677843	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv2759562	chr7:126494789-126677843	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv427805	chr7:126494789-126677843	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv608378	chr7:126570120-126597132	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1204556	LOC407835	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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