Variant report

Variant	rs9939558
Chromosome Location	chr16:31038687-31038688
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:31035621..31039590-chr16:31042058..31045187,5	K562	blood:
2	chr16:31035953..31038692-chr16:31042517..31044556,3	MCF-7	breast:
3	chr16:31037669..31039612-chr16:31083227..31085566,2	K562	blood:
4	chr16:31035739..31039592-chr16:31042123..31045685,6	K562	blood:
5	chr16:31038071..31041033-chr16:31050588..31053452,2	K562	blood:
6	chr16:31033800..31036089-chr16:31037286..31039723,2	MCF-7	breast:
7	chr16:31036111..31038797-chr16:31087110..31088802,2	K562	blood:

Variant related genes	Relation type
ENSG00000167395	Chromatin interaction
ENSG00000167394	Chromatin interaction
ENSG00000103496	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1060506	0.84[ASN][1000 genomes]
rs10871454	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1108431	1.00[ASN][1000 genomes]
rs11150604	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11640767	0.98[ASN][1000 genomes]
rs11640957	0.98[ASN][1000 genomes]
rs11642192	0.87[ASN][1000 genomes]
rs11647284	0.89[ASN][1000 genomes]
rs11647442	0.84[ASN][1000 genomes]
rs11862744	1.00[ASN][1000 genomes]
rs11864806	0.89[ASN][1000 genomes]
rs11864839	0.89[ASN][1000 genomes]
rs11865038	0.89[ASN][1000 genomes]
rs11865499	0.84[ASN][1000 genomes]
rs12445650	1.00[ASN][1000 genomes]
rs12448321	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12597511	0.82[ASN][1000 genomes]
rs12716981	0.84[ASN][1000 genomes]
rs12716982	0.84[ASN][1000 genomes]
rs12934418	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs14235	0.84[ASN][1000 genomes]
rs1549293	0.84[ASN][1000 genomes]
rs17839567	1.00[ASN][1000 genomes]
rs17839568	0.89[ASN][1000 genomes]
rs1978485	0.84[ASN][1000 genomes]
rs1978487	0.84[ASN][1000 genomes]
rs2032915	0.84[ASN][1000 genomes]
rs2288004	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303222	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2303223	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2359612	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2855475	0.84[ASN][1000 genomes]
rs28725459	0.81[ASN][1000 genomes]
rs28814987	0.89[ASN][1000 genomes]
rs2884738	0.84[ASN][1000 genomes]
rs34649473	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34898535	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35351013	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35468353	1.00[ASN][1000 genomes]
rs35713203	0.89[ASN][1000 genomes]
rs3751855	0.89[ASN][1000 genomes]
rs4468641	0.89[ASN][1000 genomes]
rs4527034	0.84[ASN][1000 genomes]
rs4889530	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4889620	0.84[ASN][1000 genomes]
rs55766044	0.84[ASN][1000 genomes]
rs55979739	1.00[ASN][1000 genomes]
rs56284083	1.00[ASN][1000 genomes]
rs56314408	0.84[ASN][1000 genomes]
rs56813533	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57434408	0.93[ASN][1000 genomes]
rs58726213	0.98[ASN][1000 genomes]
rs59061704	0.98[ASN][1000 genomes]
rs59735493	0.84[ASN][1000 genomes]
rs60996860	0.81[ASN][1000 genomes]
rs61162043	0.89[ASN][1000 genomes]
rs61320757	0.84[ASN][1000 genomes]
rs6565217	0.89[ASN][1000 genomes]
rs7187995	0.82[ASN][1000 genomes]
rs7196161	0.89[ASN][1000 genomes]
rs7196726	0.89[ASN][1000 genomes]
rs7197717	0.89[ASN][1000 genomes]
rs7199949	0.89[ASN][1000 genomes]
rs7294	0.89[ASN][1000 genomes]
rs732172	1.00[ASN][1000 genomes]
rs732173	1.00[ASN][1000 genomes]
rs73530203	0.87[ASN][1000 genomes]
rs749670	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs749671	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs749767	0.84[ASN][1000 genomes]
rs7500176	1.00[ASN][1000 genomes]
rs750952	0.89[ASN][1000 genomes]
rs8047803	0.89[ASN][1000 genomes]
rs8050894	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8056842	1.00[ASN][1000 genomes]
rs8061047	0.82[ASN][1000 genomes]
rs881929	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs889548	0.84[ASN][1000 genomes]
rs889555	0.84[ASN][1000 genomes]
rs9923231	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9925964	0.84[ASN][1000 genomes]
rs9929899	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9934438	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9936329	0.84[ASN][1000 genomes]
rs9939417	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972727	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
4	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
5	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
6	nsv833191	chr16:30864242-31048051	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	115 gene(s)	inside rSNPs	diseases
7	nsv905734	chr16:30877544-31191482	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
8	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
9	nsv457483	chr16:30903679-31191482	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
10	nsv571820	chr16:30903679-31191482	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
11	esv1797877	chr16:30948643-31188432	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
12	nsv833193	chr16:30960796-31133604	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
13	nsv916994	chr16:30971725-31078117	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9939558	HSD3B7	cis	Whole Blood	GTEx
rs9939558	KAT8	cis	Skin Sun Exposed Lower leg	GTEx
rs9939558	RP11-196G11.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31027600-31041600	Weak transcription	Spleen	Spleen
2	chr16:31027800-31043600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr16:31032200-31044000	Weak transcription	Ovary	ovary
4	chr16:31034400-31043600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr16:31034800-31043200	Weak transcription	Fetal Muscle Leg	muscle
6	chr16:31035400-31043600	Weak transcription	Fetal Intestine Small	intestine
7	chr16:31037200-31043600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr16:31037400-31040400	Weak transcription	HSMM	muscle
9	chr16:31037400-31043200	Weak transcription	A549	lung
10	chr16:31037600-31040600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr16:31037800-31043000	Weak transcription	K562	blood
12	chr16:31037800-31043200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr16:31037800-31043800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr16:31038000-31043200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr16:31038000-31043200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr16:31038200-31041400	Weak transcription	HepG2	liver

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