Variant report

Variant	rs9927309
Chromosome Location	chr16:75246419-75246420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75244083..75246522-chr16:75263997..75266825,2	MCF-7	breast:
2	chr16:75242998..75247373-chr16:75260079..75262691,3	K562	blood:
3	chr16:75242481..75244530-chr16:75245362..75248227,2	K562	blood:

Variant related genes	Relation type
ENSG00000240338	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13331385	0.92[CEU][hapmap]
rs2870463	0.99[ASN][1000 genomes]
rs3743614	0.85[CEU][hapmap]
rs59409959	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60470336	0.99[ASN][1000 genomes]
rs61634868	0.96[ASN][1000 genomes]
rs6564232	0.99[ASN][1000 genomes]
rs6564233	0.99[ASN][1000 genomes]
rs6564234	0.97[ASN][1000 genomes]
rs6564235	0.96[ASN][1000 genomes]
rs6564236	0.99[ASN][1000 genomes]
rs6564237	0.99[ASN][1000 genomes]
rs66473537	0.96[ASN][1000 genomes]
rs66502159	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66535165	0.99[ASN][1000 genomes]
rs66881382	0.99[ASN][1000 genomes]
rs67478528	0.99[ASN][1000 genomes]
rs7195852	0.94[ASN][1000 genomes]
rs7197389	0.97[ASN][1000 genomes]
rs7197746	0.99[ASN][1000 genomes]
rs7201955	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7202844	0.99[ASN][1000 genomes]
rs7202858	0.99[ASN][1000 genomes]
rs7202877	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs72802358	0.81[EUR][1000 genomes]
rs72802372	0.99[ASN][1000 genomes]
rs72802375	0.99[ASN][1000 genomes]
rs8052763	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8053595	0.97[ASN][1000 genomes]
rs8054218	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8056797	0.80[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8056814	0.81[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[YRI][hapmap];0.97[ASN][1000 genomes]
rs8057846	0.83[ASN][1000 genomes]
rs8062169	0.83[EUR][1000 genomes]
rs889512	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9921586	0.92[CEU][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs9921930	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9924354	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9940370	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[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	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
4	nsv1056082	chr16:75004990-75295847	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer 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	47 gene(s)	inside rSNPs	diseases
5	nsv833282	chr16:75154171-75330634	Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv516504	chr16:75223491-75306402	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv523405	chr16:75227969-75342846	Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	esv1806781	chr16:75235390-75307470	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv906909	chr16:75236154-75316074	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	esv1792587	chr16:75237936-75305783	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9927309	HYDIN	cis	parietal	SCAN
rs9927309	TMEM170A	cis	parietal	SCAN
rs9927309	FTSJD1	cis	cerebellum	SCAN
rs9927309	RFWD3	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75241200-75248800	Weak transcription	Fetal Intestine Small	intestine
2	chr16:75243400-75248000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:75243400-75252400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr16:75244000-75248000	Weak transcription	Placenta	Placenta
5	chr16:75244400-75252200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr16:75246000-75246800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr16:75246200-75246600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:75246200-75246600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr16:75246200-75246600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr16:75246400-75246800	Bivalent Enhancer	HepG2	liver
11	chr16:75246400-75248200	Enhancers	Pancreas	Pancrea

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