Variant report

Variant	rs17217831
Chromosome Location	chr3:46305441-46305442
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCR2-1	chr3:46304881-46305946	NONHSAT089432

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10510750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11575062	0.88[EUR][1000 genomes]
rs11919884	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919943	0.87[CEU][hapmap]
rs11926063	1.00[CEU][hapmap]
rs13065351	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13067058	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13068145	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13068271	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13070099	1.00[CEU][hapmap]
rs13071469	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13073976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13075270	1.00[CEU][hapmap]
rs13075836	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs13077302	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13078564	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13080757	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13088766	1.00[CEU][hapmap]
rs13092160	1.00[CEU][hapmap]
rs13093063	0.93[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];0.90[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];0.94[GIH][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1542755	1.00[CEU][hapmap]
rs17283712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17284138	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17284187	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1894387	0.88[EUR][1000 genomes]
rs1894388	0.88[EUR][1000 genomes]
rs2373156	1.00[CEU][hapmap]
rs28361974	0.85[AFR][1000 genomes]
rs2856762	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs28677778	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3091310	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3091314	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs3092957	0.88[EUR][1000 genomes]
rs3092958	0.88[EUR][1000 genomes]
rs3092959	0.88[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	0.83[EUR][1000 genomes]
rs34024447	0.88[EUR][1000 genomes]
rs34041956	0.88[EUR][1000 genomes]
rs34073838	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34079287	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34106161	0.88[EUR][1000 genomes]
rs34180919	0.91[EUR][1000 genomes]
rs34272024	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34351442	0.91[EUR][1000 genomes]
rs34363105	0.88[EUR][1000 genomes]
rs34406035	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34448949	0.88[EUR][1000 genomes]
rs34473395	0.88[EUR][1000 genomes]
rs34578126	0.90[EUR][1000 genomes]
rs34692251	0.83[EUR][1000 genomes]
rs34709208	0.88[EUR][1000 genomes]
rs34988015	0.91[EUR][1000 genomes]
rs35035328	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35117954	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35148665	0.91[EUR][1000 genomes]
rs35203745	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35218998	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35367413	0.88[EUR][1000 genomes]
rs35373513	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35413141	0.88[EUR][1000 genomes]
rs35438577	0.88[EUR][1000 genomes]
rs35511592	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35513549	0.83[EUR][1000 genomes]
rs35577626	0.91[EUR][1000 genomes]
rs35601704	0.88[EUR][1000 genomes]
rs35646896	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35943069	0.85[EUR][1000 genomes]
rs36048333	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36052732	0.88[EUR][1000 genomes]
rs36078103	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3749461	0.88[EUR][1000 genomes]
rs3918354	0.88[EUR][1000 genomes]
rs3918362	0.88[EUR][1000 genomes]
rs3918365	0.88[EUR][1000 genomes]
rs3918368	0.88[EUR][1000 genomes]
rs41485850	0.82[AFR][1000 genomes]
rs4473594	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4987053	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]
rs4987124	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6775046	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs6793370	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71327047	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71327048	0.91[EUR][1000 genomes]
rs71327052	0.85[EUR][1000 genomes]
rs71327053	0.86[EUR][1000 genomes]
rs71327054	0.88[EUR][1000 genomes]
rs71327055	0.88[EUR][1000 genomes]
rs71327056	0.88[EUR][1000 genomes]
rs71327057	0.88[EUR][1000 genomes]
rs71615445	0.88[EUR][1000 genomes]
rs71622511	0.98[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	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7651539	1.00[CEU][hapmap]
rs916092	0.82[CHB][hapmap]
rs9810242	0.91[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];1.00[YRI][hapmap]
rs9872023	0.93[EUR][1000 genomes]
rs9882616	0.92[AMR][1000 genomes];0.93[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
rs17217831	CCR1	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 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	chr3:46305000-46305600	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr3:46305200-46306000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr3:46305200-46306000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:46305200-46306800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:46305400-46305800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr3:46305400-46306000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:46305400-46306000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:46305400-46306000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:46305400-46309200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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