Variant report

Variant	rs13065543
Chromosome Location	chr3:119377893-119377894
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	EP300	chr3:119377802-119380796	SK-N-SH	brain:	n/a	chr3:119378444-119378451 chr3:119378091-119378105

No.	Distal block	Cell Line	Cell type
1	chr3:119371913..119374680-chr3:119377229..119379559,2	MCF-7	breast:
2	chr3:119377678..119379207-chr3:119382196..119384974,2	MCF-7	breast:
3	chr3:119375924..119378034-chr3:119380150..119381686,2	K562	blood:
4	chr3:119375861..119378454-chr3:119387094..119389806,2	K562	blood:

Variant related genes	Relation type
POPDC2	TF binding region
ENSG00000121577	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs13062540	0.95[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs13065893	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1317259	0.80[ASN][1000 genomes]
rs1880040	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1880041	0.82[ASN][1000 genomes]
rs2629395	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2629409	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2670296	0.86[ASN][1000 genomes]
rs2698282	0.85[ASN][1000 genomes]
rs3749416	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3749417	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3772134	0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4327424	0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs4687871	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4688023	0.85[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs484809	1.00[CEU][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs523476	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs552244	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs571352	0.90[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs6438542	0.82[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6785698	0.82[ASN][1000 genomes]
rs6794579	0.81[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs6807079	0.95[CHD][hapmap];0.86[GIH][hapmap];0.81[ASN][1000 genomes]
rs693397	0.86[ASN][1000 genomes]
rs7613999	0.81[ASN][1000 genomes]
rs7633444	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs8007	1.00[CEU][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1014394	chr3:119360506-119412275	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs13065543	EAF2	cis	parietal	SCAN
rs13065543	C3orf15	cis	lymphoblastoid	seeQTL
rs13065543	POPDC2	Cis_1M	lymphoblastoid	RTeQTL
rs13065543	POPDC2	cis	lymphoblastoid	seeQTL
rs13065543	POPDC2	cis	multi-tissue	Pritchard
rs13065543	POPDC2	cis	lung	GTEx
rs13065543	POPDC2	cis	Thyroid	GTEx
rs13065543	PARP14	cis	cerebellum	SCAN
rs13065543	PLA1A	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119349800-119378800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:119352000-119378600	Weak transcription	Thymus	Thymus
3	chr3:119354000-119387600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:119356200-119389000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:119356800-119390000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:119357200-119383800	Weak transcription	Primary B cells from cord blood	blood
9	chr3:119357800-119386400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
11	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
12	chr3:119361200-119378800	Weak transcription	Fetal Thymus	thymus
13	chr3:119361200-119394400	Weak transcription	Brain Angular Gyrus	brain
14	chr3:119361400-119378800	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:119362400-119387400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:119362600-119378400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:119362600-119383800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:119363200-119389400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:119363200-119389800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:119365200-119387400	Weak transcription	Liver	Liver
21	chr3:119367200-119378800	Weak transcription	Gastric	stomach
22	chr3:119367200-119381800	Weak transcription	Fetal Lung	lung
23	chr3:119367400-119378000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:119367400-119378600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:119367400-119378800	Weak transcription	Pancreas	Pancrea
26	chr3:119367600-119378200	Weak transcription	Fetal Intestine Large	intestine
27	chr3:119367600-119389200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:119367600-119391200	Weak transcription	Fetal Brain Female	brain
29	chr3:119367800-119378000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr3:119367800-119385400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:119367800-119386600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:119367800-119388800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:119368000-119386000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr3:119368200-119388200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:119371600-119379200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:119371800-119378200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:119371800-119378800	Weak transcription	Spleen	Spleen
38	chr3:119372000-119378200	Weak transcription	Lung	lung
39	chr3:119373200-119378200	Weak transcription	Adipose Nuclei	Adipose
40	chr3:119373400-119388800	Weak transcription	Aorta	Aorta
41	chr3:119374000-119378800	Active TSS	Right Atrium	heart
42	chr3:119374400-119378400	Transcr. at gene 5' and 3'	Left Ventricle	heart
43	chr3:119374600-119379600	ZNF genes & repeats	Fetal Heart	heart
44	chr3:119374800-119389000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:119375400-119378200	Weak transcription	Placenta	Placenta
46	chr3:119375400-119381600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:119375800-119381400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:119376000-119380000	Active TSS	Colon Smooth Muscle	Colon
49	chr3:119376200-119379800	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr3:119376400-119378600	Genic enhancers	GM12878-XiMat	blood

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