Variant report

Variant	rs610932
Chromosome Location	chr11:59939307-59939308
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:59926779..59928855-chr11:59938111..59940679,2	K562	blood:

Variant related genes	Relation type
ENSG00000254952	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs107903	0.93[CEU][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10897011	0.81[EUR][1000 genomes]
rs11230180	0.81[EUR][1000 genomes]
rs1125357	0.81[CEU][hapmap]
rs11605427	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs12453	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs1303615	0.94[ASW][hapmap];0.93[CEU][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1303621	0.89[ASW][hapmap];0.93[CEU][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1441586	0.83[ASW][hapmap];0.93[CEU][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17529983	0.81[CEU][hapmap]
rs17602572	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs1786137	0.82[EUR][1000 genomes]
rs1820430	0.81[EUR][1000 genomes]
rs1834549	0.81[EUR][1000 genomes]
rs1834550	0.80[EUR][1000 genomes]
rs1834551	0.80[EUR][1000 genomes]
rs2081545	0.81[EUR][1000 genomes]
rs2278867	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2847663	0.85[CEU][hapmap]
rs2847667	0.88[CEU][hapmap]
rs476722	0.93[CEU][hapmap];0.89[JPT][hapmap]
rs483629	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs487997	0.83[EUR][1000 genomes]
rs502419	0.93[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs502581	0.93[CEU][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs504272	0.89[EUR][1000 genomes]
rs510518	0.89[EUR][1000 genomes]
rs512495	0.85[EUR][1000 genomes]
rs514266	0.87[EUR][1000 genomes]
rs516478	1.00[CEU][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs521952	0.92[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs525794	0.93[CEU][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs534273	0.89[EUR][1000 genomes]
rs540170	0.93[CEU][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs555635	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs556917	0.93[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs56201148	0.81[EUR][1000 genomes]
rs563803	0.87[EUR][1000 genomes]
rs564912	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs569046	0.92[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs574695	0.93[CEU][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs574704	0.92[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs574798	0.87[EUR][1000 genomes]
rs580064	0.82[CEU][hapmap]
rs580817	0.83[EUR][1000 genomes]
rs581133	0.93[CEU][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs583296	0.93[CEU][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs583791	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs595481	0.92[CEU][hapmap]
rs602396	0.93[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs606588	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs617135	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs617916	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs624663	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs631853	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs632185	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs634475	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs636147	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs652354	0.89[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs662196	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs667897	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684961	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs688030	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs72918674	0.84[EUR][1000 genomes]
rs7926954	0.86[EUR][1000 genomes]
rs7933202	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs7935829	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs7946992	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832173	chr11:59788884-59940560	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv468579	chr11:59814287-59975400	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv555150	chr11:59814287-59975400	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv33843	chr11:59908131-59945334	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv832174	chr11:59909267-60073908	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv524137	chr11:59936979-59947252	Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Alzheimer's disease	21460840	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs610932	GNG3	cis	parietal	SCAN
rs610932	FAM111A	cis	parietal	SCAN
rs610932	MTA2	cis	cerebellum	SCAN
rs610932	SNORD27	cis	cerebellum	SCAN
rs610932	SLC43A3	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59935600-59940400	Enhancers	HUVEC	blood vessel
2	chr11:59935800-59947200	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr11:59937000-59943000	Weak transcription	Adipose Nuclei	Adipose
4	chr11:59937000-59943400	Weak transcription	Spleen	Spleen
5	chr11:59937200-59941800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:59937200-59946600	Genic enhancers	Primary monocytes fromperipheralblood	blood
7	chr11:59937200-59949800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr11:59938400-59946600	Weak transcription	Primary B cells from cord blood	blood
9	chr11:59938600-59943400	Genic enhancers	Monocytes-CD14+_RO01746	blood

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