Variant report

Variant	rs410469
Chromosome Location	chr2:32476992-32476993
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:32469608..32472298-chr2:32474844..32477443,2	K562	blood:
2	chr2:32476245..32477748-chr2:32507604..32509921,2	K562	blood:
3	chr2:32474270..32479271-chr2:32479320..32483848,6	K562	blood:
4	chr2:32463297..32465974-chr2:32475784..32478393,2	K562	blood:
5	chr2:32470343..32473625-chr2:32476011..32478727,4	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11678119	0.91[MEX][hapmap]
rs11691939	0.92[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12614686	0.91[MEX][hapmap]
rs12996943	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13006495	0.85[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13013695	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs17011801	0.93[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs177082	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs186135	0.81[AMR][1000 genomes]
rs212682	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs212683	0.81[AMR][1000 genomes]
rs212684	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs212689	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs212690	0.82[EUR][1000 genomes]
rs212691	0.82[EUR][1000 genomes]
rs212696	0.82[EUR][1000 genomes]
rs212736	1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs212742	0.84[AMR][1000 genomes]
rs212747	0.82[AMR][1000 genomes]
rs212751	0.93[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs212754	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs212761	0.85[CEU][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2280968	0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs2294178	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34197800	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs375050	0.93[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3769605	0.92[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap]
rs385076	0.83[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs462878	0.93[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs56322034	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6543648	0.82[EUR][1000 genomes]
rs6723154	0.91[MEX][hapmap]
rs6756085	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs686005	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7562653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7574000	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs805831	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2422335	chr2:32412330-33200581	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv2667	chr2:32444810-32489755	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv1002120	chr2:32470452-32539443	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1004279	chr2:32470452-32543369	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs410469	SLC30A6	cis	cerebellum	SCAN
rs410469	NLRC4	cis	lymphoblastoid	seeQTL
rs410469	SLC30A6	cis	parietal	SCAN
rs410469	NLRC4	cis	Lymphoblastoid	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32443000-32483600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:32443200-32483800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:32447400-32483800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr2:32448800-32484800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:32452200-32479400	Weak transcription	Adipose Nuclei	Adipose
6	chr2:32460000-32477000	Weak transcription	Placenta	Placenta
7	chr2:32463600-32487000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr2:32470600-32477000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:32475000-32481200	Weak transcription	Fetal Heart	heart
10	chr2:32475400-32477600	Strong transcription	Primary B cells from cord blood	blood
11	chr2:32476400-32484200	Weak transcription	Lung	lung
12	chr2:32476600-32478400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:32476600-32479000	Weak transcription	HepG2	liver
14	chr2:32476600-32480000	Weak transcription	Spleen	Spleen

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