Variant report

Variant	rs528211
Chromosome Location	chr11:64351721-64351722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64350444..64353414-chr11:64386038..64388659,2	MCF-7	breast:
2	chr11:64323432..64325391-chr11:64351236..64353955,2	K562	blood:
3	chr11:64350498..64353447-chr11:64359000..64361623,2	MCF-7	breast:
4	11:64349180-64353532..11:64523887-64530985	Hela-S3	cervix:
5	11:64349180-64353532..11:64402707-64415880	Hela-S3	cervix:
6	11:64349180-64353532..11:64415880-64426617	K562	blood:
7	11:64349180-64353532..11:64489786-64499245	K562	blood:
8	11:64349180-64353532..11:64501239-64517861	K562	blood:

Variant related genes	Relation type
ENSG00000068976	Chromatin interaction
ENSG00000068831	Chromatin interaction
ENSG00000110076	Chromatin interaction
ENSG00000237410	Chromatin interaction
ENSG00000168065	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10792441	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10792443	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10897518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11231825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11231845	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11602903	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11606370	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11607663	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12362590	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12365089	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12786214	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12802649	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1529909	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2021860	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277311	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2360872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2360873	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2666559	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35195142	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825016	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3825018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs475642	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs477138	1.00[JPT][hapmap]
rs492175	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4930556	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs495130	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs500531	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs504915	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs505802	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs506338	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs518053	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs519090	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs524023	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs526338	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs531763	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs537246	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs538737	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs544838	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs552307	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs555456	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs559946	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs561193	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7102344	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7932437	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs80841	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs893006	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs893007	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9734313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035485	chr11:64228847-64354869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897692	chr11:64305452-64386526	Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
3	nsv897693	chr11:64305452-64440920	Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	esv2422214	chr11:64312491-64483418	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv832188	chr11:64315368-64485209	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv468596	chr11:64334114-64527080	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv555195	chr11:64334114-64527080	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
9	nsv818842	chr11:64345448-64546391	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
10	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
11	esv3437606	chr11:64347576-64351774	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs528211	NRXN2	cis	lung	GTEx
rs528211	EHD1	cis	cerebellum	SCAN
rs528211	CDC42BPG	cis	parietal	SCAN
rs528211	SF1	cis	lymphoblastoid	seeQTL
rs528211	POLA2	cis	cerebellum	SCAN
rs528211	TBC1D10C	cis	cerebellum	SCAN
rs528211	MALAT1	cis	parietal	SCAN
rs528211	DDB1	cis	parietal	SCAN
rs528211	TMEM138	cis	cerebellum	SCAN
rs528211	SF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64350200-64352200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:64350400-64351800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:64350600-64352200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr11:64351400-64352200	Enhancers	Spleen	Spleen
5	chr11:64351600-64351800	Enhancers	HepG2	liver

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