Variant report

Variant	rs557809
Chromosome Location	chr3:146215917-146215918
allele	A/G
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	NFYB	chr3:146215688-146216095	GM12878	blood:	n/a	n/a
2	SP1	chr3:146215586-146215974	GM12878	blood:	n/a	n/a
3	NFYA	chr3:146215594-146215994	K562	blood:	n/a	chr3:146215822-146215840
4	NFYB	chr3:146215696-146215999	Hela-S3	cervix:	n/a	n/a
5	NFYB	chr3:146215402-146216086	K562	blood:	n/a	n/a
6	SP1	chr3:146215561-146215935	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:146214293..146216886-chr3:146219168..146220915,2	MCF-7	breast:

Variant related genes	Relation type
PLSCR2	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1054736	0.86[ASN][1000 genomes]
rs11708619	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11716510	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11916950	0.95[ASN][1000 genomes]
rs13065970	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35102814	0.82[ASN][1000 genomes]
rs35296568	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35783134	0.86[ASN][1000 genomes]
rs4681324	0.85[ASN][1000 genomes]
rs4681327	0.90[EUR][1000 genomes]
rs473794	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474803	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488053	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs491900	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs498201	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs500995	0.95[ASN][1000 genomes]
rs506974	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512845	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs514287	0.95[ASN][1000 genomes]
rs518330	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs523849	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524720	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527708	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533625	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs534092	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs536474	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs536619	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536737	0.95[ASN][1000 genomes]
rs544178	0.96[EUR][1000 genomes]
rs546430	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs563385	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs568302	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs575834	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272708	0.89[AMR][1000 genomes]
rs62274675	0.80[ASN][1000 genomes]
rs968634	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968635	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv877622	chr3:146131961-146219740	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3448053	chr3:146186791-146262066	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	esv3523751	chr3:146186838-146261806	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv3523753	chr3:146186838-146261806	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	esv2496437	chr3:146186902-146262961	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv3416587	chr3:146191303-146222138	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146211400-146221200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:146214200-146235400	Weak transcription	Right Atrium	heart
3	chr3:146214800-146216000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:146214800-146216200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:146214800-146220600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:146215000-146216000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:146215000-146216000	ZNF genes & repeats	Fetal Thymus	thymus
8	chr3:146215000-146220400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:146215000-146220800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:146215200-146216000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:146215400-146216200	Enhancers	K562	blood
12	chr3:146215800-146216000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr3:146215800-146216000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr3:146215800-146216000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr3:146215800-146216000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr3:146215800-146216000	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr3:146215800-146216200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr3:146215800-146216200	Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr3:146215800-146216200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr3:146215800-146216200	Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr3:146215800-146216200	Enhancers	Thymus	Thymus
22	chr3:146215800-146216400	Active TSS	Primary T cells from cord blood	blood
23	chr3:146215800-146216400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr3:146215800-146216400	Flanking Active TSS	Dnd41	blood
25	chr3:146215800-146216400	Active TSS	Monocytes-CD14+_RO01746	blood
26	chr3:146215800-146217600	Enhancers	Rectal Mucosa Donor 31	rectum

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