Variant report

Variant	rs2329845
Chromosome Location	chr21:46087164-46087165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr21:46086985-46087166	MCF10A-Er-Src	breast:	n/a	chr21:46087037-46087048
2	FOS	chr21:46086629-46087212	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr21:46086733-46087171	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
KRTAP12-2	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10854464	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11088958	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11700616	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11911323	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12626853	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13046471	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13048478	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13049382	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13051885	0.86[JPT][hapmap]
rs13052189	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13052715	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1883042	0.80[GIH][hapmap]
rs2329844	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838612	0.80[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs2838613	0.85[ASN][1000 genomes]
rs2838622	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838634	0.84[JPT][hapmap]
rs28735609	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4050979	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs7276859	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7509675	0.82[JPT][hapmap]
rs8126811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8130076	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9967974	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9984686	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065798	chr21:45941000-46097463	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv869108	chr21:45941000-46097463	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv544476	chr21:45941000-46097463	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv913950	chr21:45985068-46097463	Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2329845	FAM3B	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46079400-46089600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:46086800-46087200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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