Variant report

Variant	rs3782360
Chromosome Location	chr12:49256792-49256793
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49256473-49256952	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr12:49256726-49257085	H1-hESC	embryonic stem cell:	n/a	chr12:49256914-49256924 chr12:49256899-49256910 chr12:49256913-49256929 chr12:49256913-49256925 chr12:49256912-49256929 chr12:49256914-49256936
3	POLR2A	chr12:49255873-49258188	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:49253272-49258971	A549	lung:	n/a	n/a
5	POLR2A	chr12:49256327-49256962	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49250166..49253023-chr12:49256244..49259199,2	K562	blood:
2	chr12:49256218..49258210-chr12:49380440..49382850,2	MCF-7	breast:

Variant related genes	Relation type
RND1	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1045340	0.84[JPT][hapmap]
rs10783285	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875882	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565933	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2446972	1.00[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs3759148	1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs4760597	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760598	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760599	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760639	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469373	chr12:49256792-49285390	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
2	nsv558832	chr12:49256792-49285390	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3782360	PLEKHA9	cis	parietal	SCAN
rs3782360	RND1	cis	multi-tissue	Pritchard
rs3782360	FKBP11	cis	parietal	SCAN
rs3782360	FKBP11	cis	cerebellum	SCAN
rs3782360	ANO6	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49246600-49258600	Weak transcription	Small Intestine	intestine
2	chr12:49247200-49257000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:49247200-49257800	Weak transcription	Stomach Mucosa	stomach
4	chr12:49247200-49258000	Weak transcription	Brain Substantia Nigra	brain
5	chr12:49247200-49258600	Weak transcription	Esophagus	oesophagus
6	chr12:49247200-49258600	Weak transcription	Right Ventricle	heart
7	chr12:49247200-49258800	Weak transcription	Right Atrium	heart
8	chr12:49247200-49259000	Weak transcription	Ovary	ovary
9	chr12:49251600-49257800	Weak transcription	Spleen	Spleen
10	chr12:49251800-49257400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr12:49252000-49257400	Weak transcription	GM12878-XiMat	blood
12	chr12:49252400-49257800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr12:49253600-49257000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:49253800-49258200	Weak transcription	HepG2	liver
15	chr12:49254800-49257400	Genic enhancers	Liver	Liver
16	chr12:49254800-49259000	Transcr. at gene 5' and 3'	A549	lung
17	chr12:49255400-49256800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:49255400-49257200	Weak transcription	Adipose Nuclei	Adipose
19	chr12:49255400-49257800	Weak transcription	Fetal Intestine Large	intestine
20	chr12:49255400-49258000	Weak transcription	Pancreas	Pancrea
21	chr12:49255600-49257800	Weak transcription	Fetal Intestine Small	intestine
22	chr12:49255800-49260200	Active TSS	Brain Angular Gyrus	brain
23	chr12:49256000-49256800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:49256000-49257400	Weak transcription	Primary B cells from cord blood	blood
25	chr12:49256000-49258200	Flanking Active TSS	Fetal Brain Female	brain
26	chr12:49256000-49258400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:49256000-49258400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:49256000-49260200	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr12:49256200-49256800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr12:49256200-49257400	Flanking Active TSS	Brain Germinal Matrix	brain
31	chr12:49256200-49257800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:49256200-49257800	Active TSS	Brain Hippocampus Middle	brain
33	chr12:49256200-49259000	Flanking Active TSS	Fetal Brain Male	brain
34	chr12:49256200-49259400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:49256200-49259800	Active TSS	Brain Cingulate Gyrus	brain
36	chr12:49256400-49256800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:49256400-49257000	Enhancers	Lung	lung
38	chr12:49256400-49257400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr12:49256400-49257600	Enhancers	Fetal Kidney	kidney
40	chr12:49256400-49258000	Enhancers	H9 Cell Line	embryonic stem cell
41	chr12:49256400-49258000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:49256400-49258400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:49256400-49258800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:49256400-49260200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr12:49256600-49256800	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr12:49256600-49256800	Weak transcription	Gastric	stomach
47	chr12:49256600-49257200	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr12:49256600-49257200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:49256600-49257400	Genic enhancers	H1 Cell Line	embryonic stem cell
50	chr12:49256600-49257800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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