Variant report

Variant	rs3909456
Chromosome Location	chr5:42962350-42962351
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:42958938..42960616-chr5:42961964..42963478,2	MCF-7	breast:
2	chr5:42962325..42964680-chr5:43067049..43069391,2	K562	blood:
3	chr5:42961475..42963380-chr5:42978584..42980242,2	K562	blood:

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction
ENSG00000177738	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10036916	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10064003	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10522	0.95[JPT][hapmap]
rs10941598	0.83[ASN][1000 genomes]
rs10941604	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10941605	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11743123	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs11743246	0.91[EUR][1000 genomes]
rs11747435	0.81[ASN][1000 genomes]
rs11747714	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11954543	0.84[EUR][1000 genomes]
rs11958008	0.81[ASN][1000 genomes]
rs12697439	0.95[JPT][hapmap]
rs13169690	0.90[CHD][hapmap];0.95[JPT][hapmap]
rs13170208	0.95[JPT][hapmap]
rs13179934	0.89[ASN][1000 genomes]
rs1542369	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs1574407	0.95[JPT][hapmap]
rs160709	0.89[CHD][hapmap];0.95[JPT][hapmap]
rs1624415	0.86[JPT][hapmap]
rs17300176	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs178415	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs186323	0.94[ASN][1000 genomes]
rs186324	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs188693	0.81[ASN][1000 genomes]
rs1902101	0.81[ASN][1000 genomes]
rs2100473	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs222060	0.89[CHD][hapmap];0.95[JPT][hapmap]
rs2253450	0.81[ASN][1000 genomes]
rs2329995	0.89[CHD][hapmap];0.95[JPT][hapmap]
rs2432097	0.83[ASN][1000 genomes]
rs2548334	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2548336	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2548339	0.94[ASN][1000 genomes]
rs2548341	0.91[ASN][1000 genomes]
rs2548343	0.92[ASN][1000 genomes]
rs2548345	0.93[ASN][1000 genomes]
rs2548346	0.90[ASN][1000 genomes]
rs2548349	0.81[ASN][1000 genomes]
rs2548350	0.88[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2548353	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2548356	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2548374	0.83[ASN][1000 genomes]
rs2548382	0.81[ASN][1000 genomes]
rs2603620	0.93[ASN][1000 genomes]
rs2603625	0.83[ASN][1000 genomes]
rs2603626	0.83[ASN][1000 genomes]
rs2603627	0.83[ASN][1000 genomes]
rs2603628	0.83[ASN][1000 genomes]
rs2603629	0.83[ASN][1000 genomes]
rs2603630	0.83[ASN][1000 genomes]
rs2603631	0.83[ASN][1000 genomes]
rs2603632	0.83[ASN][1000 genomes]
rs2603633	0.83[ASN][1000 genomes]
rs2603644	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2603649	0.83[ASN][1000 genomes]
rs2603650	0.83[ASN][1000 genomes]
rs2603651	0.82[ASN][1000 genomes]
rs2603656	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2876993	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2882295	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs309909	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs309911	0.82[ASN][1000 genomes]
rs309912	0.83[ASN][1000 genomes]
rs309914	0.95[JPT][hapmap]
rs309922	0.91[ASN][1000 genomes]
rs309923	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs309924	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs309925	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs309926	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs309927	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs309938	0.83[ASN][1000 genomes]
rs309939	0.83[ASN][1000 genomes]
rs309940	0.83[ASN][1000 genomes]
rs309948	0.94[ASN][1000 genomes]
rs309950	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs3849696	0.81[ASN][1000 genomes]
rs3849697	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3893725	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4092293	0.90[CHD][hapmap];0.95[JPT][hapmap]
rs4092294	0.90[CHD][hapmap];0.95[JPT][hapmap]
rs512921	0.86[JPT][hapmap]
rs557076	0.86[JPT][hapmap]
rs567884	0.86[JPT][hapmap]
rs643307	0.95[JPT][hapmap]
rs6451660	0.95[JPT][hapmap]
rs6451661	0.95[JPT][hapmap]
rs6451662	0.92[CHD][hapmap];0.95[JPT][hapmap]
rs6859096	0.91[EUR][1000 genomes]
rs6861491	0.83[ASN][1000 genomes]
rs6879130	0.95[JPT][hapmap]
rs6880163	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6882794	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6883097	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6889150	0.82[ASN][1000 genomes]
rs6889271	0.83[ASN][1000 genomes]
rs6890457	0.83[CEU][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6890469	0.82[ASW][hapmap];0.81[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6892422	0.86[JPT][hapmap]
rs6895732	0.83[ASN][1000 genomes]
rs6899257	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724430	0.90[JPT][hapmap]
rs768441	0.95[JPT][hapmap]
rs7707797	0.83[ASN][1000 genomes]
rs7715065	1.00[JPT][hapmap]
rs7733383	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782971	0.86[JPT][hapmap]
rs782978	0.86[JPT][hapmap]
rs903391	0.86[JPT][hapmap]
rs9292862	0.92[CHD][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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	esv1806082	chr5:42906572-42967215	Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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
14	nsv528880	chr5:42940230-42967215	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv515883	chr5:42949688-42967215	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	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
17	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
18	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3909456	LOC646887	cis	multi-tissue	Pritchard
rs3909456	LOC643977	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 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	chr5:42960600-42963000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:42961800-42966200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr5:42962000-42962400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr5:42962200-42984400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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