Variant report

Variant	rs6441961
Chromosome Location	chr3:46352384-46352385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCR1-1	chr3:46352082-46353413	NONHSAT089433

Extended variants
information (count: 85 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10865940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11711054	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11923720	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13081845	0.85[EUR][1000 genomes]
rs13084656	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs13096142	0.85[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs1388604	0.90[JPT][hapmap]
rs1799865	0.96[CEU][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs2097282	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2097284	0.91[EUR][1000 genomes]
rs2157057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2157058	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2157059	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2187669	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2187670	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2213291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2213292	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3092962	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs3092963	0.96[CEU][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs3138042	0.91[EUR][1000 genomes]
rs34148191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34193387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34505903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34997146	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35053103	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35465430	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35510257	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35675823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35971655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36030342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36048784	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3762823	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs3918358	0.96[CEU][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs4134396	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683198	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683211	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4683215	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4683218	0.80[ASN][1000 genomes]
rs62244813	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62244827	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62244828	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62244840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62244848	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441950	0.90[JPT][hapmap]
rs6441953	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441958	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6441959	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6441960	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6441962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441963	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6441964	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441971	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs6441972	0.91[EUR][1000 genomes]
rs6767895	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6771900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775208	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783993	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6785878	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6785981	0.91[EUR][1000 genomes]
rs6788723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794300	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6802288	0.83[EUR][1000 genomes]
rs71615444	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7371987	0.90[JPT][hapmap];0.81[MEX][hapmap]
rs7372094	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7374654	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7374671	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7432080	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs743660	0.81[MEX][hapmap]
rs7612940	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7626249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs762789	0.84[EUR][1000 genomes]
rs7634816	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7635588	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs963045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9813756	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9842716	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs9852052	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9853223	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs9856098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats 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

Variant related diseases (count:1)

Disease	PMID	Source
Celiac disease	18311140	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6441961	KLHL18	cis	parietal	SCAN
rs6441961	DALRD3	cis	cerebellum	SCAN
rs6441961	RBM5	cis	parietal	SCAN
rs6441961	ABHD5	cis	parietal	SCAN
rs6441961	TRAIP	cis	cerebellum	SCAN
rs6441961	CCR5	trans	multi-tissue	Pritchard
rs6441961	SLC25A20	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46350600-46352400	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr3:46350800-46367600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:46352200-46352400	Weak transcription	Spleen	Spleen
4	chr3:46352200-46352800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr3:46352200-46353000	Enhancers	NHEK	skin

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