Variant report

Variant	rs2629409
Chromosome Location	chr3:119386760-119386761
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:119383822-119386921	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119384409..119387165-chr3:119391759..119393266,2	K562	blood:
2	chr3:119297190..119298785-chr3:119385064..119387274,2	MCF-7	breast:
3	chr3:119366599..119368508-chr3:119385647..119388287,2	MCF-7	breast:
4	chr3:119380893..119382995-chr3:119385609..119387430,2	MCF-7	breast:
5	chr3:119384220..119388638-chr3:119390311..119393902,4	K562	blood:
6	chr3:119380060..119382164-chr3:119384940..119387375,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POPDC2-1	chr3:119385766-119386938	NONHSAT091399

No data

Variant related genes	Relation type
POPDC2	TF binding region
ENSG00000272967	Chromatin interaction
ENSG00000144843	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11720605	0.92[EUR][1000 genomes]
rs11914676	0.85[JPT][hapmap]
rs11923223	0.86[JPT][hapmap]
rs12490779	0.81[JPT][hapmap]
rs13062540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065543	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs13065893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1317259	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16830291	0.85[JPT][hapmap]
rs1872432	0.85[JPT][hapmap]
rs1880040	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1880041	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046430	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2280578	0.85[JPT][hapmap]
rs2629395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2629397	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2670296	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2688629	0.85[JPT][hapmap]
rs2688631	0.85[JPT][hapmap]
rs2688633	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2692618	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2698282	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3749416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3749417	0.95[ASN][1000 genomes]
rs3772134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4327424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687871	0.92[ASN][1000 genomes]
rs4688023	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4688024	0.85[JPT][hapmap]
rs484809	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs523476	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540420	0.81[JPT][hapmap]
rs552244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs571352	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs572119	0.85[JPT][hapmap]
rs62265884	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6438541	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438542	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6766563	0.90[JPT][hapmap]
rs6782253	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6785698	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794484	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6794579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803814	0.80[JPT][hapmap]
rs6807079	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs693397	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7613999	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7626940	0.90[JPT][hapmap]
rs7633444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8007	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs940181	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv460834	chr3:119384163-119458851	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv591390	chr3:119384163-119458851	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2629409	POPDC2	cis	Thyroid	GTEx
rs2629409	POPDC2	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119354000-119387600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:119356200-119389000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:119356800-119390000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
5	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
7	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
8	chr3:119361200-119394400	Weak transcription	Brain Angular Gyrus	brain
9	chr3:119362400-119387400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:119363200-119389400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:119363200-119389800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:119365200-119387400	Weak transcription	Liver	Liver
13	chr3:119367600-119389200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:119367600-119391200	Weak transcription	Fetal Brain Female	brain
15	chr3:119367800-119388800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:119368200-119388200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:119373400-119388800	Weak transcription	Aorta	Aorta
18	chr3:119374800-119389000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:119377400-119387200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:119377400-119387400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:119379000-119387400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:119379200-119391800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:119379200-119392400	Weak transcription	Esophagus	oesophagus
24	chr3:119379200-119392400	Weak transcription	Gastric	stomach
25	chr3:119379400-119388600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:119379600-119387400	Weak transcription	Fetal Intestine Large	intestine
27	chr3:119379800-119391800	Weak transcription	Thymus	Thymus
28	chr3:119380000-119391800	Weak transcription	Lung	lung
29	chr3:119380000-119391800	Weak transcription	Ovary	ovary
30	chr3:119380000-119391800	Weak transcription	Pancreas	Pancrea
31	chr3:119380000-119391800	Weak transcription	Spleen	Spleen
32	chr3:119380000-119392000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:119380400-119391000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:119381000-119392000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:119381800-119389400	Weak transcription	A549	lung
36	chr3:119382000-119388800	Weak transcription	Right Atrium	heart
37	chr3:119382200-119388000	Weak transcription	Fetal Lung	lung
38	chr3:119382200-119390600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:119382400-119387400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:119382400-119390000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:119382400-119390600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:119382400-119391000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:119382400-119391800	Weak transcription	Fetal Stomach	stomach
44	chr3:119382600-119388800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:119382600-119391800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:119383800-119390600	Weak transcription	Brain Germinal Matrix	brain
47	chr3:119383800-119393800	Strong transcription	Primary B cells from cord blood	blood
48	chr3:119384000-119387400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:119384000-119387400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:119384000-119387600	Weak transcription	NHDF-Ad	bronchial

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