Variant report

Variant	rs8031394
Chromosome Location	chr15:75964226-75964227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75964154-75964245	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:75963778-75966547	Hela-S3	cervix:	n/a	n/a
3	MAZ	chr15:75963794-75966405	IMR90	lung:	n/a	chr15:75966377-75966387 chr15:75966378-75966387 chr15:75966378-75966387 chr15:75965682-75965692 chr15:75966379-75966386
4	POLR2A	chr15:75963541-75966466	U87	brain:	n/a	n/a
5	POLR2A	chr15:75964170-75964535	MCF10A-Er-Src	breast:	n/a	n/a
6	GATA3	chr15:75964029-75964417	T-47D	breast:	n/a	n/a
7	POLR2A	chr15:75964032-75966447	U87	brain:	n/a	n/a
8	POLR2A	chr15:75964035-75964679	ProgFib	skin:	n/a	n/a
9	POLR2A	chr15:75963672-75964256	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr15:75961392-75968208	U87	brain:	n/a	n/a
11	POLR2A	chr15:75963030-75967116	U87	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:75963026..75964801-chr15:75971008..75973448,2	K562	blood:
2	chr15:75659530..75662177-chr15:75962521..75965318,2	K562	blood:
3	chr15:75743241..75745218-chr15:75963628..75965414,2	MCF-7	breast:
4	chr15:75927186..75935349-chr15:75957229..75967736,17	MCF-7	breast:
5	chr15:75943051..75945736-chr15:75963392..75964991,2	MCF-7	breast:
6	chr15:75937430..75939214-chr15:75963572..75966390,2	MCF-7	breast:
7	chr15:75951981..75955869-chr15:75961912..75967583,8	MCF-7	breast:
8	chr15:75954503..75957935-chr15:75961367..75965113,3	K562	blood:
9	chr15:75744190..75746911-chr15:75963679..75965801,2	MCF-7	breast:
10	chr15:75953678..75955508-chr15:75964203..75966702,2	K562	blood:
11	chr15:75957411..75961529-chr15:75962208..75964451,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260892	TF binding region
ENSG00000140400	Chromatin interaction
ENSG00000260206	Chromatin interaction
ENSG00000177971	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000169375	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11632887	0.90[GIH][hapmap]
rs11638663	0.90[GIH][hapmap]
rs12592229	0.88[ASN][1000 genomes]
rs4886454	0.83[ASN][1000 genomes]
rs4886730	0.84[ASN][1000 genomes]
rs61754538	0.83[ASN][1000 genomes]
rs72732862	0.88[ASN][1000 genomes]
rs8028183	0.88[ASN][1000 genomes]
rs8041033	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
4	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS 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 miRNA target site	161 gene(s)	inside rSNPs	diseases
5	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
6	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
7	esv1813854	chr15:75898640-76002392	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
9	nsv904391	chr15:75930757-76001654	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
10	nsv904392	chr15:75930757-76039262	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
11	nsv904393	chr15:75932177-76001654	Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
12	nsv984485	chr15:75932760-75965433	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	nsv904394	chr15:75948671-76039262	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv904395	chr15:75957928-75984095	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
15	nsv904396	chr15:75961518-76071105	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8031394	PTPN9	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75953000-75969600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:75953200-75964600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:75953200-75964800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr15:75953400-75964800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:75954200-75965000	Weak transcription	Brain Hippocampus Middle	brain
6	chr15:75954400-75964800	Weak transcription	Brain Substantia Nigra	brain
7	chr15:75954400-75964800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:75955600-75965400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:75956200-75966400	Enhancers	HMEC	breast
10	chr15:75956600-75964600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:75956600-75967000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:75957800-75967200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr15:75958200-75967200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:75958400-75967000	Enhancers	Fetal Muscle Leg	muscle
15	chr15:75959200-75964800	Weak transcription	Fetal Lung	lung
16	chr15:75959400-75965000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:75959400-75967600	Weak transcription	Liver	Liver
18	chr15:75959800-75965000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:75960000-75965000	Weak transcription	Brain Anterior Caudate	brain
20	chr15:75960000-75965600	Weak transcription	Aorta	Aorta
21	chr15:75960200-75964400	Weak transcription	Fetal Intestine Small	intestine
22	chr15:75960200-75964400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr15:75960200-75964600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:75960200-75964800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:75960200-75964800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:75960200-75964800	Weak transcription	Colonic Mucosa	Colon
27	chr15:75960200-75965200	Weak transcription	Psoas Muscle	Psoas
28	chr15:75960200-75966200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr15:75960400-75964800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr15:75960400-75964800	Weak transcription	HSMMtube	muscle
31	chr15:75960400-75965000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr15:75960400-75965000	Weak transcription	HSMM	muscle
33	chr15:75961000-75968200	Enhancers	NHDF-Ad	bronchial
34	chr15:75961200-75966600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:75961800-75964400	Weak transcription	Fetal Intestine Large	intestine
36	chr15:75962000-75964600	Weak transcription	A549	lung
37	chr15:75962000-75964800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:75962000-75965400	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr15:75962200-75964600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:75962200-75964600	Weak transcription	Stomach Mucosa	stomach
41	chr15:75962400-75968600	Enhancers	Adipose Nuclei	Adipose
42	chr15:75962400-75968800	Enhancers	Right Ventricle	heart
43	chr15:75962400-75969000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr15:75962600-75964800	Weak transcription	K562	blood
45	chr15:75962800-75966000	Enhancers	Lung	lung
46	chr15:75962800-75966200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:75963000-75965400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:75963200-75964600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr15:75963200-75965400	Enhancers	Fetal Muscle Trunk	muscle
50	chr15:75963200-75968400	Enhancers	Placenta	Placenta

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