Variant report

Variant	rs783544
Chromosome Location	chr15:83240293-83240294
allele	A/C
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	chr15:83239371-83241116	U87	brain:	n/a	n/a
2	MXI1	chr15:83239563-83241354	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr15:83240131-83241116	U87	brain:	n/a	n/a
4	POLR2A	chr15:83240257-83240957	H1-neurons	neurons:	n/a	n/a
5	MAX	chr15:83240292-83240961	SK-N-SH	brain:	n/a	n/a
6	MXI1	chr15:83239714-83241131	IMR90	lung:	n/a	n/a
7	POLR2A	chr15:83240050-83240957	U87	brain:	n/a	n/a
8	USF1	chr15:83240279-83240706	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAZ	chr15:83239241-83241683	IMR90	lung:	n/a	n/a
10	POLR2A	chr15:83240073-83240957	U87	brain:	n/a	n/a
11	ZNF263	chr15:83239839-83241557	HEK293-T-REx	kidney:	n/a	chr15:83241307-83241316 chr15:83240612-83240633 chr15:83240614-83240623
12	CHD2	chr15:83240056-83240691	H1-hESC	embryonic stem cell:	n/a	chr15:83240612-83240622
13	SIN3A	chr15:83240021-83240802	H1-hESC	embryonic stem cell:	n/a	chr15:83240568-83240579
14	JUND	chr15:83240197-83240807	H1-hESC	embryonic stem cell:	n/a	n/a
15	REST	chr15:83240019-83240956	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr15:83240206-83241159	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:83238387..83241317-chr15:83241503..83245353,3	K562	blood:

Variant related genes	Relation type
CPEB1	TF binding region
ENSG00000214575	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11631182	0.85[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap]
rs11633991	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs11635044	0.92[CHB][hapmap]
rs11635442	0.90[CEU][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11635460	0.92[CHB][hapmap];0.93[CHD][hapmap]
rs11635476	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11635624	0.93[GIH][hapmap]
rs11638815	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11639010	0.84[AMR][1000 genomes]
rs1267656	0.85[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1431717	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1877242	0.92[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap]
rs2379997	0.82[CHB][hapmap]
rs35734713	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4779041	0.93[GIH][hapmap]
rs4779048	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4779049	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs62011675	0.81[AFR][1000 genomes]
rs6603030	0.84[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7171180	0.93[GIH][hapmap]
rs7182320	0.92[CHB][hapmap];0.93[CHD][hapmap];0.80[JPT][hapmap]
rs783542	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8033106	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427965	chr15:82741381-83310525	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv428309	chr15:82741381-83310525	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv2758391	chr15:82879646-83310525	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	esv2760046	chr15:82879646-83310525	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1035899	chr15:83108446-83315731	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833071	chr15:83123646-83310510	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs783544	RASGRF1	cis	cerebellum	SCAN
rs783544	PSMA4	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83222800-83240600	Weak transcription	Aorta	Aorta
2	chr15:83236000-83243600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:83239400-83240600	Flanking Active TSS	NHLF	lung
4	chr15:83239400-83241000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:83239400-83241400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:83239600-83240400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:83239600-83240400	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr15:83239600-83240600	Flanking Active TSS	Osteobl	bone
9	chr15:83239600-83240800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:83239600-83241200	Flanking Active TSS	NHDF-Ad	bronchial
11	chr15:83239600-83241400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:83239800-83240400	Enhancers	H9 Cell Line	embryonic stem cell
13	chr15:83239800-83240400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr15:83239800-83240400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:83239800-83240400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr15:83239800-83240400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:83239800-83240400	Flanking Active TSS	Fetal Lung	lung
18	chr15:83239800-83240400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr15:83239800-83240600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:83239800-83240600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:83239800-83240600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
22	chr15:83239800-83240600	Flanking Active TSS	HSMMtube	muscle
23	chr15:83239800-83240800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:83239800-83240800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:83239800-83240800	Enhancers	Lung	lung
26	chr15:83239800-83240800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr15:83239800-83240800	Flanking Active TSS	NH-A	brain
28	chr15:83239800-83241000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr15:83239800-83241000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:83239800-83241000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr15:83239800-83241000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr15:83239800-83241000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr15:83239800-83241000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:83239800-83241000	Flanking Active TSS	Fetal Brain Female	brain
35	chr15:83239800-83241000	Flanking Active TSS	HSMM	muscle
36	chr15:83239800-83241200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:83239800-83241200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:83239800-83241200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:83239800-83241200	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr15:83240000-83240400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr15:83240000-83240400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr15:83240000-83240400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr15:83240000-83240400	Enhancers	Adipose Nuclei	Adipose
44	chr15:83240000-83240400	Active TSS	Colonic Mucosa	Colon
45	chr15:83240000-83240400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
46	chr15:83240000-83240400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr15:83240000-83240400	Enhancers	Fetal Kidney	kidney
48	chr15:83240000-83240400	Enhancers	Left Ventricle	heart
49	chr15:83240000-83240400	Enhancers	Pancreas	Pancrea
50	chr15:83240000-83240400	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum

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