Variant report

Variant	rs4902439
Chromosome Location	chr14:66405430-66405431
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:66404813..66406809-chr14:66413591..66416552,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12431878	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55737164	0.87[ASN][1000 genomes]
rs60135008	0.96[ASN][1000 genomes]
rs61989516	0.92[ASN][1000 genomes]
rs7142317	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7146427	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7155478	0.80[EUR][1000 genomes]
rs7156170	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.98[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.88[ASN][1000 genomes]
rs7158156	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8013361	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
2	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
3	esv3366524	chr14:65924360-66423862	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	nsv817409	chr14:66220075-66990168	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv564953	chr14:66287921-67046960	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv1050485	chr14:66308283-67109270	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv530775	chr14:66316836-67079049	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv530793	chr14:66317036-67078908	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	nsv1046455	chr14:66345369-66848234	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1043864	chr14:66372458-66845503	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv917338	chr14:66376591-66841403	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4902439	GPX2	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:66403200-66408000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr14:66403400-66405600	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr14:66403400-66405600	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr14:66403400-66405600	Enhancers	Dnd41	blood
5	chr14:66403400-66406400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr14:66403400-66406400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr14:66403400-66408200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr14:66403600-66405600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr14:66404200-66407800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr14:66404400-66405600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr14:66404400-66406800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr14:66404600-66406400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr14:66404600-66408000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr14:66404600-66408200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr14:66404600-66415000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr14:66404600-66415200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr14:66404800-66407200	Enhancers	Primary T cells from cord blood	blood
18	chr14:66404800-66407200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr14:66404800-66408000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr14:66404800-66408200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr14:66404800-66410000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr14:66405000-66405600	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr14:66405000-66416400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr14:66405400-66407200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr14:66405400-66410200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr14:66405400-66416600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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