Variant report

Variant	rs6893520
Chromosome Location	chr5:101650861-101650862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10434748	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10434749	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10463981	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10515326	1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap]
rs1098806	0.83[ASN][1000 genomes]
rs12658397	0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap]
rs1376905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1376907	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1452058	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17333350	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs174414	0.80[JPT][hapmap]
rs1982418	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2113092	0.80[JPT][hapmap]
rs2123136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2161601	0.90[JPT][hapmap]
rs2263376	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2400800	0.92[ASN][1000 genomes]
rs2548724	0.89[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2600824	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2600825	0.89[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2600827	0.84[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2600828	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2600830	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2600832	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2600834	0.89[GIH][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2600835	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs261101	0.90[JPT][hapmap]
rs3096196	0.89[JPT][hapmap]
rs3114659	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs370176	0.84[GIH][hapmap];0.90[JPT][hapmap]
rs390614	0.87[GIH][hapmap];0.90[JPT][hapmap]
rs420900	0.89[JPT][hapmap]
rs431778	0.84[GIH][hapmap];0.90[JPT][hapmap]
rs432190	0.90[JPT][hapmap]
rs438617	0.94[JPT][hapmap]
rs4386713	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs452857	0.84[GIH][hapmap];0.90[JPT][hapmap]
rs4703224	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57415604	0.84[ASN][1000 genomes]
rs58644688	0.84[ASN][1000 genomes]
rs62369303	0.83[ASN][1000 genomes]
rs62369304	0.84[ASN][1000 genomes]
rs62372171	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62372211	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62372300	0.92[ASN][1000 genomes]
rs6596486	0.81[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs6881112	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6884141	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs709370	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7710414	0.87[ASN][1000 genomes]
rs7714927	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7728630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7733501	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7734060	0.84[CEU][hapmap];0.95[CHB][hapmap]
rs841920	0.83[ASN][1000 genomes]
rs841922	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs841926	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs841932	0.93[ASN][1000 genomes]
rs841934	0.90[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882505	chr5:101397849-101652251	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1028787	chr5:101432086-101718569	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv817537	chr5:101489151-101992104	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1016176	chr5:101534391-102333606	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv537831	chr5:101534391-102333606	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv522882	chr5:101596633-101782930	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1029894	chr5:101620079-102516827	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv462324	chr5:101633610-101729504	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv599189	chr5:101633610-101729504	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1015892	chr5:101633610-101730439	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1020531	chr5:101637963-101730439	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv599190	chr5:101638381-101733177	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv882510	chr5:101638381-101733177	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6893520	PAM	cis	cerebellum	SCAN
rs6893520	PAM	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:101647800-101651600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr5:101648600-101654000	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr5:101648800-101653800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr5:101649000-101654200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr5:101650200-101651200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:101650800-101651800	Weak transcription	Primary hematopoietic stem cells	blood

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