Variant report

Variant	rs61408596
Chromosome Location	chr3:138668692-138668693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr3:138668219-138668698	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr3:138667529-138669545	H1-hESC	embryonic stem cell:	n/a	n/a
3	SUZ12	chr3:138668250-138670232	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr3:138668016-138668720	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:138668098-138669582	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr3:138667014-138669383	H1-hESC	embryonic stem cell:	n/a	n/a
7	SUZ12	chr3:138662343-138670118	NT2-D1	testis:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138667185..138669200-chr3:139015942..139017731,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPS22-3	chr3:138668354-138669670	NONHSAT092347

No data

Variant related genes	Relation type
FOXL2	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12493711	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2018794	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58880010	0.85[EUR][1000 genomes]
rs58908753	0.85[EUR][1000 genomes]
rs59081321	0.86[AMR][1000 genomes]
rs60291969	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60515064	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60650442	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60838328	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61750361	0.85[EUR][1000 genomes]
rs6439831	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66475108	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67626684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780823	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72976944	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72976956	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7629926	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7639122	0.82[AMR][1000 genomes]
rs7649365	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs931250	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv877540	chr3:138645013-138670695	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv877541	chr3:138645013-138673922	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv877542	chr3:138645013-138750904	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138664600-138668800	Active TSS	Ovary	ovary
2	chr3:138666800-138668800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:138667400-138668800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
4	chr3:138667400-138668800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
5	chr3:138667600-138669600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:138667800-138669000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:138667800-138669000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
8	chr3:138667800-138669400	Bivalent Enhancer	Fetal Brain Male	brain
9	chr3:138667800-138669600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr3:138667800-138669600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
11	chr3:138667800-138671600	Weak transcription	Hela-S3	cervix
12	chr3:138667800-138672800	Weak transcription	K562	blood
13	chr3:138668000-138668800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:138668000-138668800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr3:138668000-138668800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
16	chr3:138668000-138668800	Bivalent Enhancer	Fetal Stomach	stomach
17	chr3:138668000-138669400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr3:138668200-138668800	Bivalent Enhancer	Primary B cells from cord blood	blood
19	chr3:138668200-138668800	Bivalent Enhancer	NH-A	brain
20	chr3:138668200-138669000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
21	chr3:138668200-138669000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:138668200-138669600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:138668200-138669600	Bivalent Enhancer	Fetal Thymus	thymus
24	chr3:138668200-138669800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
25	chr3:138668400-138668800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:138668400-138668800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
27	chr3:138668400-138668800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
28	chr3:138668400-138668800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
29	chr3:138668400-138668800	Bivalent Enhancer	Adipose Nuclei	Adipose
30	chr3:138668400-138668800	Bivalent Enhancer	Brain Angular Gyrus	brain
31	chr3:138668400-138668800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
32	chr3:138668400-138668800	Bivalent Enhancer	Colonic Mucosa	Colon
33	chr3:138668400-138668800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr3:138668400-138668800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr3:138668400-138668800	Bivalent Enhancer	Fetal Muscle Leg	muscle
36	chr3:138668400-138668800	Bivalent Enhancer	Left Ventricle	heart
37	chr3:138668400-138668800	Bivalent Enhancer	Rectal Smooth Muscle	rectum
38	chr3:138668400-138668800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
39	chr3:138668400-138668800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
40	chr3:138668400-138668800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
41	chr3:138668400-138669000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:138668400-138669000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:138668400-138669000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
44	chr3:138668400-138669400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
45	chr3:138668400-138669400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
46	chr3:138668400-138669400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
47	chr3:138668400-138669400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
48	chr3:138668400-138669400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:138668400-138669400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:138668400-138669600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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