Variant report

Variant	rs4146884
Chromosome Location	chr11:74799470-74799471
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74796178..74800020-chr11:74800917..74805286,4	K562	blood:
2	chr11:74798344..74800296-chr11:74811269..74812884,2	K562	blood:

Variant related genes	Relation type
ENSG00000137491	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10899068	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236316	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236317	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236322	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236325	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236359	0.85[CEU][hapmap]
rs1893839	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2187435	0.90[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2712781	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2712787	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2712789	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2712790	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2712796	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2712805	0.90[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2712807	0.81[ASN][1000 genomes]
rs2712819	0.85[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs2851064	0.90[CEU][hapmap];0.89[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs2851074	0.84[CEU][hapmap]
rs2851085	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2851094	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2851096	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2851102	0.85[ASN][1000 genomes]
rs2851108	0.85[ASN][1000 genomes]
rs3017932	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3018832	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34806493	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4456280	0.84[CHB][hapmap]
rs7112183	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7122948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs753171	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7933093	0.82[AFR][1000 genomes]
rs949072	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9634028	0.86[EUR][1000 genomes];0.97[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	esv3478707	chr11:74782633-74842791	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	esv3478718	chr11:74782633-74842791	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv975203	chr11:74786322-74799744	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4146884	XRRA1	cis	parietal	SCAN
rs4146884	XRRA1	cis	lymphoblastoid	seeQTL
rs4146884	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs4146884	UCP2	cis	parietal	SCAN
rs4146884	XRRA1	cis	cerebellum	SCAN
rs4146884	INPPL1	cis	parietal	SCAN
rs4146884	PHOX2A	cis	parietal	SCAN
rs4146884	P2RY2	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74794200-74802000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:74799400-74801800	Strong transcription	K562	blood

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