Variant report

Variant	rs7552289
Chromosome Location	chr1:76238441-76238442
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76236456..76238614-chr1:76251949..76253787,2	K562	blood:
2	chr1:76237665..76239915-chr1:76250102..76252794,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137955	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000207241	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11161465	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs11161598	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163917	0.81[EUR][1000 genomes]
rs11163928	0.81[EUR][1000 genomes]
rs1146598	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146607	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146609	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146610	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146617	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146630	0.86[ASN][1000 genomes]
rs1146634	0.93[GIH][hapmap];0.90[TSI][hapmap]
rs1146635	0.87[GIH][hapmap]
rs1146636	0.93[GIH][hapmap];0.90[TSI][hapmap]
rs1146644	0.93[GIH][hapmap];0.90[TSI][hapmap]
rs12022011	0.88[CEU][hapmap]
rs12043473	0.84[GIH][hapmap]
rs12044025	0.81[CEU][hapmap]
rs12045299	0.86[CEU][hapmap]
rs12092388	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12732722	0.86[CEU][hapmap]
rs12744608	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs1323735	0.80[EUR][1000 genomes]
rs1332786	0.81[EUR][1000 genomes]
rs1463812	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211713	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs211719	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs5745323	0.81[EUR][1000 genomes]
rs6593520	0.87[GIH][hapmap]
rs6695055	0.86[CEU][hapmap]
rs7533542	0.81[EUR][1000 genomes]
rs7548991	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs814875	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap]
rs814876	0.95[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap]
rs9660848	0.86[CEU][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	esv2763563	chr1:76229839-76245374	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7552289	MSH4	cis	cerebellum	SCAN
rs7552289	RABGGTB	cis	parietal	SCAN
rs7552289	ACADM	cis	cerebellum	SCAN
rs7552289	RABGGTB	cis	lymphoblastoid	seeQTL
rs7552289	AK5	cis	parietal	SCAN
rs7552289	MSH4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76227400-76249800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:76227800-76239600	Weak transcription	GM12878-XiMat	blood
3	chr1:76232800-76243200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:76234000-76241000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:76234600-76241200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:76238000-76241200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:76238200-76241000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:76238200-76241400	Weak transcription	NHEK	skin

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