Variant report

Variant	rs9927295
Chromosome Location	chr16:31077409-31077410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:31077185-31077886	HL-60	blood:	n/a	n/a
2	POLR2A	chr16:31077276-31077530	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31044379..31046301-chr16:31075916..31077490,2	MCF-7	breast:
2	chr16:31076020..31078080-chr16:31104345..31106297,2	MCF-7	breast:
3	chr16:31076302..31081402-chr16:31082512..31087316,9	K562	blood:
4	chr16:31076535..31078976-chr16:31190040..31192835,3	MCF-7	breast:
5	chr16:31043007..31053782-chr16:31072765..31087431,40	MCF-7	breast:
6	chr16:31072102..31073706-chr16:31075876..31078559,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF668	TF binding region
ENSG00000167397	Chromatin interaction
ENSG00000255439	Chromatin interaction
ENSG00000167394	Chromatin interaction
ENSG00000103496	Chromatin interaction
ENSG00000089280	Chromatin interaction
ENSG00000232748	Chromatin interaction
ENSG00000167395	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs11645814	0.92[MEX][hapmap]
rs11865038	0.82[YRI][hapmap]
rs17708472	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17855606	0.93[MEX][hapmap]
rs17881535	0.83[AMR][1000 genomes]
rs2054214	1.00[GIH][hapmap];0.84[MEX][hapmap]
rs2359674	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3751855	0.82[YRI][hapmap]
rs45599534	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6565214	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7196726	0.82[YRI][hapmap]
rs7197717	0.82[YRI][hapmap]
rs7199949	0.82[YRI][hapmap]
rs72785521	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72785525	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72785535	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72800854	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72800858	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8046978	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8047104	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9788865	0.85[CEU][hapmap];0.95[GIH][hapmap]

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	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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv905740	chr16:31066249-31232437	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
14	nsv905741	chr16:31066249-31247924	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9927295	PHACTR2	trans	lymphoblastoid	seeQTL
rs9927295	STX1B	cis	parietal	SCAN
rs9927295	ZNF48	cis	cerebellum	SCAN
rs9927295	STX4	cis	lymphoblastoid	seeQTL
rs9927295	STX1B	cis	cerebellum	SCAN
rs9927295	ZNF668	cis	cerebellum	SCAN
rs9927295	QPRT	cis	parietal	SCAN
rs9927295	YPEL3	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31046000-31083200	Weak transcription	Right Atrium	heart
2	chr16:31051400-31083000	Weak transcription	Fetal Lung	lung
3	chr16:31052000-31083400	Weak transcription	Primary B cells from cord blood	blood
4	chr16:31054000-31083200	Weak transcription	Fetal Kidney	kidney
5	chr16:31070400-31082600	Weak transcription	Fetal Brain Male	brain
6	chr16:31073600-31082800	Weak transcription	HepG2	liver
7	chr16:31073600-31083000	Weak transcription	Small Intestine	intestine
8	chr16:31073600-31083200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr16:31073600-31083200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr16:31073600-31083200	Weak transcription	Brain Substantia Nigra	brain
11	chr16:31073800-31083400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr16:31074400-31078000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr16:31075400-31078400	Enhancers	Fetal Muscle Trunk	muscle
14	chr16:31075400-31084000	Weak transcription	Ovary	ovary
15	chr16:31075600-31082800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr16:31075600-31083000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr16:31075600-31083000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr16:31075600-31083000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr16:31075600-31083000	Weak transcription	Brain Angular Gyrus	brain
20	chr16:31075600-31083000	Weak transcription	Brain Anterior Caudate	brain
21	chr16:31075600-31083000	Weak transcription	Brain Hippocampus Middle	brain
22	chr16:31075600-31083000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr16:31075600-31083200	Weak transcription	Liver	Liver
24	chr16:31075600-31083400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr16:31075600-31083600	Weak transcription	Gastric	stomach
26	chr16:31075600-31083800	Weak transcription	Aorta	Aorta
27	chr16:31075800-31077800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr16:31075800-31077800	Enhancers	Placenta	Placenta
29	chr16:31075800-31080200	Weak transcription	Pancreas	Pancrea
30	chr16:31075800-31082600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr16:31075800-31082800	Weak transcription	Fetal Brain Female	brain
32	chr16:31075800-31083000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr16:31075800-31083000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr16:31075800-31083000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr16:31075800-31083000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr16:31075800-31083000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr16:31075800-31083200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr16:31075800-31083400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr16:31075800-31083400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr16:31075800-31083400	Weak transcription	Fetal Intestine Large	intestine
41	chr16:31076000-31080200	Weak transcription	Dnd41	blood
42	chr16:31076000-31082800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr16:31076200-31077800	Enhancers	Primary T cells fromperipheralblood	blood
44	chr16:31076200-31077800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr16:31076200-31078000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr16:31076200-31078000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr16:31076200-31079400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr16:31076200-31082800	Weak transcription	Thymus	Thymus
49	chr16:31076200-31083000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr16:31076400-31077600	Enhancers	Skeletal Muscle Male	skeletal muscle

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