Variant report

Variant	rs309923
Chromosome Location	chr5:42969129-42969130
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:42969037..42971723-chr5:42975649..42977780,2	K562	blood:
2	chr5:42967335..42969495-chr5:43037103..43039655,2	K562	blood:
3	chr5:42967781..42970008-chr5:42973643..42976450,2	K562	blood:

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10036916	0.91[ASN][1000 genomes]
rs10064003	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10522	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10941604	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10941605	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11747435	0.86[ASN][1000 genomes]
rs11747714	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11958008	0.86[ASN][1000 genomes]
rs12697439	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs13169690	0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs13170208	0.83[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs13178479	0.80[ASN][1000 genomes]
rs13179934	0.95[ASN][1000 genomes]
rs1542369	0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs1574407	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs160709	0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs1618891	0.86[JPT][hapmap]
rs1624415	0.86[JPT][hapmap]
rs178415	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs186323	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs186324	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1902101	0.86[ASN][1000 genomes]
rs2100473	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs222060	0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs2247280	0.80[ASN][1000 genomes]
rs2253450	0.86[ASN][1000 genomes]
rs2329995	0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs2548334	0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[ASN][1000 genomes]
rs2548336	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs2548339	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548341	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2548343	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548345	0.99[ASN][1000 genomes]
rs2548346	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2548349	0.86[ASN][1000 genomes]
rs2548350	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2548353	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2548356	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2548373	0.80[ASN][1000 genomes]
rs2603620	0.98[ASN][1000 genomes]
rs2603634	0.80[ASN][1000 genomes]
rs2603644	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2603651	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2603656	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2876993	0.81[ASN][1000 genomes]
rs2882295	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2924819	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs309909	0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs309914	0.83[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs309922	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs309924	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs309925	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs309926	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs309927	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs309948	0.94[ASN][1000 genomes]
rs309950	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs316404	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs316408	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs316413	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs316414	0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs316416	0.80[ASN][1000 genomes]
rs3849697	0.91[ASN][1000 genomes]
rs3893725	0.81[ASN][1000 genomes]
rs3909456	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4092293	0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs4092294	0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.80[ASN][1000 genomes]
rs512921	0.86[JPT][hapmap]
rs557076	0.86[JPT][hapmap]
rs567884	0.86[JPT][hapmap]
rs643307	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6451660	0.83[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6451661	0.83[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6451662	0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs6879130	0.95[JPT][hapmap]
rs6880163	0.92[ASN][1000 genomes]
rs6882794	0.88[ASN][1000 genomes]
rs6883097	0.93[ASN][1000 genomes]
rs6890469	0.89[CHD][hapmap]
rs6892422	0.86[JPT][hapmap]
rs6899257	0.91[ASN][1000 genomes]
rs724430	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs768441	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7707797	0.88[ASN][1000 genomes]
rs7715065	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7733383	0.91[ASN][1000 genomes]
rs782971	0.86[JPT][hapmap]
rs782978	0.86[JPT][hapmap]
rs903391	0.86[JPT][hapmap]
rs9292862	0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	esv1813779	chr5:42906572-42992040	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	esv3346992	chr5:42921680-42970055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
11	nsv1020910	chr5:42929799-43000021	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
12	nsv537738	chr5:42929799-43000021	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
13	nsv968169	chr5:42956713-43043472	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	116 gene(s)	inside rSNPs	diseases
14	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
15	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers 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	283 gene(s)	inside rSNPs	diseases
16	nsv881436	chr5:42967215-43008917	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
17	nsv880447	chr5:42967215-43030798	Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs309923	LOC646887	cis	multi-tissue	Pritchard
rs309923	LOC643977	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42954800-42982200	Weak transcription	HUVEC	blood vessel
2	chr5:42955000-42972600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr5:42962200-42984400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:42966400-42974600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr5:42966600-42972000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr5:42966600-42972400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr5:42966800-42972200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr5:42967000-42985600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:42967400-42972200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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