Variant report

Variant	rs12934894
Chromosome Location	chr16:77319899-77319900
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:77318927..77321221-chr16:77323637..77325291,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1060547	0.92[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs11862959	1.00[YRI][hapmap]
rs12923460	0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs12925274	0.92[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs12927388	0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs12933721	0.86[JPT][hapmap]
rs12935229	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs12935394	0.88[JPT][hapmap]
rs16945428	0.92[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs16945442	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs16945453	1.00[YRI][hapmap]
rs16945456	1.00[YRI][hapmap]
rs17712926	0.92[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs17712956	0.92[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs17713119	0.88[JPT][hapmap]
rs17769663	0.93[ASN][1000 genomes]
rs17769712	0.92[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs17769754	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs17769760	0.89[JPT][hapmap]
rs17769870	0.88[JPT][hapmap]
rs34371402	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055234	chr16:77003426-77467286	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1065048	chr16:77003426-77675163	Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv2830376	chr16:77014551-77658185	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv1065149	chr16:77032082-77671890	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv1062349	chr16:77039764-77458731	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv542967	chr16:77039764-77458731	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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	27 gene(s)	inside rSNPs	diseases
7	nsv1056676	chr16:77139682-77854848	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv1066258	chr16:77229953-77521919	Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv542968	chr16:77229953-77521919	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv2761916	chr16:77277005-77555833	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1059194	chr16:77281068-77745928	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv542969	chr16:77281068-77745928	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv934211	chr16:77281069-77396084	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1065714	chr16:77285659-77385518	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12934894	ADAMTS18	cis	cerebellum	SCAN
rs12934894	FA2H	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77306200-77320000	Weak transcription	Brain Substantia Nigra	brain
2	chr16:77311600-77344200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr16:77312000-77321800	Weak transcription	HSMM	muscle
4	chr16:77312000-77336600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr16:77316000-77323200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr16:77317000-77329200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr16:77317200-77321800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:77317600-77322000	Weak transcription	HSMMtube	muscle
9	chr16:77318800-77321200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr16:77318800-77332400	Weak transcription	Ovary	ovary
11	chr16:77319400-77320000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr16:77319800-77321000	Strong transcription	Adipose Nuclei	Adipose
13	chr16:77319800-77328800	Weak transcription	Brain Angular Gyrus	brain

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