Variant report

Variant	rs4987053
Chromosome Location	chr3:46306700-46306701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCR2-1	chr3:46306640-46306712	NONHSAT089431
2	lnc-CCR2-1	chr3:46306639-46306856	NONHSAT089432

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10510750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11575062	0.86[EUR][1000 genomes]
rs11919884	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919943	0.87[CEU][hapmap]
rs11926063	1.00[CEU][hapmap]
rs13065351	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13067058	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs13068145	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13068271	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13070099	1.00[CEU][hapmap]
rs13071469	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13073976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13075270	1.00[CEU][hapmap]
rs13075836	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs13077302	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13078564	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13080757	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13088766	1.00[CEU][hapmap]
rs13092160	1.00[CEU][hapmap]
rs13093063	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13095946	1.00[CEU][hapmap]
rs13096307	1.00[CEU][hapmap]
rs13096325	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13096371	1.00[CEU][hapmap]
rs13096808	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13097340	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs13100243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1542755	1.00[CEU][hapmap]
rs17217831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17283712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17284138	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17284187	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1894387	0.86[EUR][1000 genomes]
rs1894388	0.86[EUR][1000 genomes]
rs2373156	1.00[CEU][hapmap]
rs2856762	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs28677778	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3091310	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3091314	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs3092957	0.86[EUR][1000 genomes]
rs3092958	0.86[EUR][1000 genomes]
rs3092959	0.86[EUR][1000 genomes]
rs3136667	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs3176825	1.00[CEU][hapmap]
rs3176826	1.00[CEU][hapmap]
rs3181076	1.00[CEU][hapmap]
rs3181080	1.00[CEU][hapmap]
rs33998492	0.82[EUR][1000 genomes]
rs34024447	0.86[EUR][1000 genomes]
rs34041956	0.86[EUR][1000 genomes]
rs34073838	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34079287	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34106161	0.86[EUR][1000 genomes]
rs34180919	0.90[EUR][1000 genomes]
rs34272024	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34351442	0.90[EUR][1000 genomes]
rs34363105	0.86[EUR][1000 genomes]
rs34406035	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34448949	0.86[EUR][1000 genomes]
rs34473395	0.86[EUR][1000 genomes]
rs34578126	0.88[EUR][1000 genomes]
rs34692251	0.82[EUR][1000 genomes]
rs34709208	0.86[EUR][1000 genomes]
rs34988015	0.90[EUR][1000 genomes]
rs35035328	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35117954	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35148665	0.90[EUR][1000 genomes]
rs35203745	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35218998	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35367413	0.86[EUR][1000 genomes]
rs35373513	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35413141	0.86[EUR][1000 genomes]
rs35438577	0.86[EUR][1000 genomes]
rs35511592	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35513549	0.82[EUR][1000 genomes]
rs35577626	0.90[EUR][1000 genomes]
rs35601704	0.86[EUR][1000 genomes]
rs35646896	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35943069	0.83[EUR][1000 genomes]
rs36048333	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36052732	0.86[EUR][1000 genomes]
rs36078103	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3749461	0.86[EUR][1000 genomes]
rs3918354	0.86[EUR][1000 genomes]
rs3918362	0.86[EUR][1000 genomes]
rs3918365	0.86[EUR][1000 genomes]
rs3918368	0.86[EUR][1000 genomes]
rs4473594	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6775046	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs6793370	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6803341	0.81[AMR][1000 genomes]
rs71327047	0.91[EUR][1000 genomes]
rs71327048	0.90[EUR][1000 genomes]
rs71327052	0.83[EUR][1000 genomes]
rs71327053	0.85[EUR][1000 genomes]
rs71327054	0.86[EUR][1000 genomes]
rs71327055	0.86[EUR][1000 genomes]
rs71327056	0.86[EUR][1000 genomes]
rs71327057	0.86[EUR][1000 genomes]
rs71615445	0.86[EUR][1000 genomes]
rs71622511	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620586	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs7624155	1.00[CEU][hapmap]
rs7628489	1.00[CEU][hapmap]
rs7631551	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs7649905	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7651539	1.00[CEU][hapmap]
rs916092	0.82[CHB][hapmap]
rs9810242	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9832730	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9838191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9872023	0.91[EUR][1000 genomes]
rs9882616	0.91[EUR][1000 genomes];0.84[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	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4987053	CCR1	cis	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46303400-46315200	Weak transcription	Gastric	stomach
2	chr3:46304600-46308200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:46304600-46308200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:46304600-46310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:46305200-46306800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:46305400-46309200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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