Variant report

Variant	rs484809
Chromosome Location	chr3:119366883-119366884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119363598..119365543-chr3:119365969..119367975,2	MCF-7	breast:
2	chr3:119366599..119368508-chr3:119385647..119388287,2	MCF-7	breast:
3	chr3:119356916..119358623-chr3:119366628..119369264,2	K562	blood:
4	chr3:119361516..119364108-chr3:119364269..119367239,2	K562	blood:
5	chr3:119365198..119367042-chr3:119394724..119396860,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138495	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11914676	0.81[JPT][hapmap]
rs11923223	0.81[JPT][hapmap]
rs12490779	0.85[JPT][hapmap]
rs12492456	0.85[JPT][hapmap]
rs13062540	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs13065543	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]
rs13065893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1317259	0.89[ASN][1000 genomes]
rs1403631	0.85[JPT][hapmap]
rs16830291	0.81[JPT][hapmap]
rs17203235	0.85[JPT][hapmap]
rs1872432	0.81[JPT][hapmap]
rs1880040	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1880041	0.91[ASN][1000 genomes]
rs1985121	0.85[JPT][hapmap]
rs2046430	0.89[ASN][1000 genomes]
rs2280578	0.81[JPT][hapmap]
rs2629395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2629409	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2670292	0.85[JPT][hapmap]
rs2670296	0.96[ASN][1000 genomes]
rs2688629	0.81[JPT][hapmap]
rs2688631	0.81[JPT][hapmap]
rs2698282	0.98[ASN][1000 genomes]
rs3749416	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3749417	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772134	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4234662	0.84[JPT][hapmap]
rs4327424	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4687871	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688021	0.85[JPT][hapmap]
rs4688023	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688024	0.81[JPT][hapmap]
rs523476	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs524043	0.85[JPT][hapmap]
rs525916	0.85[JPT][hapmap]
rs540420	0.85[JPT][hapmap]
rs552244	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs571352	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6438541	0.81[ASN][1000 genomes]
rs6438542	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6766563	0.85[JPT][hapmap]
rs6782253	0.88[ASN][1000 genomes]
rs6783324	0.85[JPT][hapmap]
rs6785698	0.91[ASN][1000 genomes]
rs6794579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6807079	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs693397	0.96[ASN][1000 genomes]
rs7613999	0.90[ASN][1000 genomes]
rs7626940	0.85[JPT][hapmap]
rs7633444	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs8007	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8422	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	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
5	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs484809	POPDC2	cis	multi-tissue	Pritchard
rs484809	POPDC2	cis	lung	GTEx
rs484809	PARP14	cis	cerebellum	SCAN
rs484809	POPDC2	cis	Thyroid	GTEx
rs484809	EAF2	cis	parietal	SCAN
rs484809	POPDC2	Cis_1M	lymphoblastoid	RTeQTL
rs484809	PLA1A	cis	parietal	SCAN
rs484809	POPDC2	cis	lymphoblastoid	seeQTL

Chromatin state (count:87 , 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	chr3:119352600-119367000	Weak transcription	Ovary	ovary
4	chr3:119354000-119387600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:119356200-119389000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:119356800-119390000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
8	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:119357200-119383800	Weak transcription	Primary B cells from cord blood	blood
10	chr3:119357800-119367000	Weak transcription	Fetal Intestine Large	intestine
11	chr3:119357800-119386400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:119358000-119371200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
14	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
15	chr3:119358200-119372600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:119358400-119367000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:119358400-119376600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:119358600-119371600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:119358600-119372400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:119358600-119376800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr3:119360800-119367800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:119361200-119367000	Weak transcription	Gastric	stomach
23	chr3:119361200-119369000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:119361200-119378800	Weak transcription	Fetal Thymus	thymus
25	chr3:119361200-119394400	Weak transcription	Brain Angular Gyrus	brain
26	chr3:119361400-119372600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr3:119361400-119378800	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:119362200-119367000	Weak transcription	Lung	lung
29	chr3:119362200-119371400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:119362400-119368600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:119362400-119387400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:119362600-119378400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:119362600-119383800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:119363200-119389400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:119363200-119389800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:119364800-119367400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:119365000-119367400	Weak transcription	Stomach Mucosa	stomach
38	chr3:119365000-119368000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:119365200-119367200	Transcr. at gene 5' and 3'	Fetal Heart	heart
40	chr3:119365200-119367600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:119365200-119372200	Enhancers	Right Atrium	heart
42	chr3:119365200-119387400	Weak transcription	Liver	Liver
43	chr3:119365400-119367400	Genic enhancers	Adipose Nuclei	Adipose
44	chr3:119365400-119367400	Genic enhancers	Stomach Smooth Muscle	stomach
45	chr3:119365400-119367800	Genic enhancers	Fetal Muscle Leg	muscle
46	chr3:119365400-119368800	Strong transcription	Primary T cells from cord blood	blood
47	chr3:119365400-119369000	Genic enhancers	Colon Smooth Muscle	Colon
48	chr3:119365600-119367200	Enhancers	HSMMtube	muscle
49	chr3:119365600-119367400	Genic enhancers	Placenta	Placenta
50	chr3:119365600-119367800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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