Variant report

Variant	rs9289721
Chromosome Location	chr3:146254836-146254837
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:146254293-146255337	MCF10A-Er-Src	breast:	n/a	n/a
2	NR3C1	chr3:146254634-146254879	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr3:146254067-146256812	K562	blood:	n/a	n/a
4	POLR2A	chr3:146254399-146255969	A549	lung:	n/a	n/a
5	POLR2A	chr3:146254635-146255682	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:146254404-146255221	MCF10A-Er-Src	breast:	n/a	n/a
7	NR3C1	chr3:146254628-146254847	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr3:146254123-146256380	K562	blood:	n/a	n/a
9	POLR2A	chr3:146254776-146254864	Hela-S3	cervix:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:146254115..146256698-chr3:146261297..146263941,3	MCF-7	breast:
2	chr3:146245382..146249214-chr3:146253354..146257434,4	K562	blood:
3	chr3:146251866..146257697-chr3:146260468..146262994,8	MCF-7	breast:
4	chr3:146247932..146249479-chr3:146254766..146256376,2	MCF-7	breast:

No data

Variant related genes	Relation type
PLSCR1	TF binding region
ENSG00000188313	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1124628	1.00[ASN][1000 genomes]
rs1553628	1.00[ASN][1000 genomes]
rs1606175	1.00[ASN][1000 genomes]
rs17752579	1.00[ASN][1000 genomes]
rs62272756	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73159170	1.00[ASN][1000 genomes]
rs73159193	1.00[ASN][1000 genomes]
rs73159198	1.00[ASN][1000 genomes]
rs73160903	1.00[ASN][1000 genomes]
rs73160904	1.00[ASN][1000 genomes]
rs73160905	1.00[ASN][1000 genomes]
rs73160906	1.00[ASN][1000 genomes]
rs73160909	1.00[ASN][1000 genomes]
rs73160912	1.00[ASN][1000 genomes]
rs73160972	1.00[ASN][1000 genomes]
rs73160973	1.00[ASN][1000 genomes]
rs73160976	1.00[ASN][1000 genomes]
rs73160977	1.00[ASN][1000 genomes]
rs73160981	1.00[ASN][1000 genomes]
rs9864107	0.86[AMR][1000 genomes];0.91[EUR][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	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
2	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
3	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
4	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

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146225400-146255000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:146225400-146256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:146225400-146257000	Weak transcription	Right Ventricle	heart
4	chr3:146225400-146260800	Weak transcription	NH-A	brain
5	chr3:146225600-146258600	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:146229000-146259600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:146229800-146257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:146231600-146257200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:146231600-146258600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:146231600-146259000	Weak transcription	Brain Angular Gyrus	brain
11	chr3:146231600-146260800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:146232000-146257400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr3:146232000-146259600	Weak transcription	NHDF-Ad	bronchial
14	chr3:146232800-146256000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:146233000-146255200	Weak transcription	Esophagus	oesophagus
16	chr3:146233000-146259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:146233000-146261400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:146233600-146259200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:146234400-146258000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:146240400-146257200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:146241800-146255000	Weak transcription	Lung	lung
22	chr3:146241800-146258600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:146244800-146258200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:146246600-146257200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:146247200-146260800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:146248800-146260800	Weak transcription	HSMM	muscle
27	chr3:146249000-146259600	Weak transcription	Aorta	Aorta
28	chr3:146249400-146260800	Weak transcription	NHLF	lung
29	chr3:146250000-146257200	Weak transcription	A549	lung
30	chr3:146250600-146256600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:146250600-146256600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:146250600-146257000	Weak transcription	Primary T cells from cord blood	blood
33	chr3:146250600-146257400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:146250600-146257600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:146250600-146258400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:146250600-146259600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr3:146250600-146260000	Weak transcription	Thymus	Thymus
38	chr3:146250600-146260800	Weak transcription	Fetal Kidney	kidney
39	chr3:146250800-146256800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:146250800-146257000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:146251000-146259200	Weak transcription	Osteobl	bone
42	chr3:146251400-146256800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:146251400-146257600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr3:146251600-146259600	Weak transcription	Colonic Mucosa	Colon
45	chr3:146252000-146256600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:146252200-146256200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:146252200-146256800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr3:146252600-146258800	Weak transcription	NHEK	skin
49	chr3:146252600-146259600	Weak transcription	Psoas Muscle	Psoas
50	chr3:146252800-146255000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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