Variant report

Variant	rs4486677
Chromosome Location	chr12:8669116-8669117
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10161057	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10841788	0.89[ASN][1000 genomes]
rs11045982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11045983	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11045985	0.85[CEU][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs12297600	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12302626	0.83[EUR][1000 genomes]
rs12305960	0.81[ASN][1000 genomes]
rs12310530	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12310576	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28485567	0.86[EUR][1000 genomes]
rs4304840	0.85[CEU][hapmap];0.91[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs4534636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55898717	0.81[ASN][1000 genomes]
rs57832572	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61706479	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7135960	0.85[CEU][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs7314690	0.85[CEU][hapmap];0.91[GIH][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs74059866	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7954950	0.81[ASN][1000 genomes]
rs7976134	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040302	chr12:8245364-8695612	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541397	chr12:8245364-8695612	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1044543	chr12:8449100-8792569	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1039504	chr12:8494944-8780137	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv557342	chr12:8599397-8774527	Enhancers Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription 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	10 gene(s)	inside rSNPs	diseases
6	nsv933050	chr12:8602789-8775989	Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv518125	chr12:8615809-8671274	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1035270	chr12:8619562-8674062	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv933555	chr12:8627165-8775989	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	8 gene(s)	inside rSNPs	diseases
10	nsv933639	chr12:8627243-8775989	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv526021	chr12:8662809-8671274	Enhancers Active TSS Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1048336	chr12:8663355-8797018	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4486677	CLEC4A	cis	cerebellum	SCAN
rs4486677	PEX5	cis	parietal	SCAN
rs4486677	AICDA	cis	cerebellum	SCAN
rs4486677	KCNA5	cis	parietal	SCAN
rs4486677	MLF2	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8667600-8671000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:8668200-8669200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:8668200-8673000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
4	chr12:8669000-8669200	Genic enhancers	Monocytes-CD14+_RO01746	blood
5	chr12:8669000-8669400	Bivalent Enhancer	Brain Cingulate Gyrus	brain

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