Variant report

Variant	rs60295689
Chromosome Location	chr3:138492823-138492824
allele	C/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	POLR2A	chr3:138492584-138494502	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:138487382..138490287-chr3:138491067..138493545,2	K562	blood:
2	chr3:138491707..138493497-chr3:138496731..138499046,3	K562	blood:
3	chr3:138491707..138493497-chr3:138496731..138499014,2	K562	blood:

Variant related genes	Relation type
PIK3CB	TF binding region
GAPDHP39	TF binding region
ENSG00000051382	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12107289	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12108068	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28473201	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3729699	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56382670	1.00[AFR][1000 genomes]
rs56927625	0.89[AFR][1000 genomes]
rs57216562	1.00[AMR][1000 genomes]
rs58671569	1.00[AMR][1000 genomes]
rs59797415	1.00[AMR][1000 genomes]
rs59813438	1.00[AMR][1000 genomes]
rs60850836	1.00[AMR][1000 genomes]
rs60987624	0.89[AFR][1000 genomes]
rs61301555	0.82[AFR][1000 genomes]
rs6795773	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72972909	1.00[AFR][1000 genomes]
rs72972913	0.98[AFR][1000 genomes]
rs72972920	0.92[AFR][1000 genomes]
rs72972926	0.84[AFR][1000 genomes]
rs72988878	1.00[AMR][1000 genomes]
rs72990507	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72990541	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72990552	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72990569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72990577	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73866224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7648802	0.84[AFR][1000 genomes]
rs7649131	0.90[AFR][1000 genomes];1.00[AMR][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	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	nsv1000927	chr3:138423543-138632596	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	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

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138369000-138493000	Weak transcription	Fetal Lung	lung
2	chr3:138393800-138515000	Weak transcription	Aorta	Aorta
3	chr3:138408400-138499200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:138460400-138493200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:138475400-138494200	Weak transcription	Psoas Muscle	Psoas
6	chr3:138476400-138494000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:138482800-138493000	Weak transcription	Right Atrium	heart
8	chr3:138484800-138493000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:138487400-138493000	Weak transcription	Right Ventricle	heart
10	chr3:138487400-138493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:138487600-138493000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:138487600-138493000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:138487600-138493000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:138487600-138494200	Weak transcription	Colonic Mucosa	Colon
15	chr3:138487600-138494200	Weak transcription	Ovary	ovary
16	chr3:138487800-138493200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:138487800-138493200	Weak transcription	Left Ventricle	heart
18	chr3:138487800-138493400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:138488000-138493000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:138488000-138493000	Weak transcription	Adipose Nuclei	Adipose
21	chr3:138488000-138493000	Weak transcription	Fetal Brain Female	brain
22	chr3:138488000-138493400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:138488000-138493400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:138488000-138493800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:138488000-138493800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:138488000-138494000	Weak transcription	Pancreas	Pancrea
27	chr3:138488000-138494200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:138488000-138494200	Weak transcription	Esophagus	oesophagus
29	chr3:138488000-138494200	Weak transcription	Lung	lung
30	chr3:138488000-138497000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:138488000-138497200	Weak transcription	Gastric	stomach
32	chr3:138488000-138498600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:138488000-138499800	Weak transcription	Thymus	Thymus
34	chr3:138488000-138504600	Weak transcription	Primary B cells from cord blood	blood
35	chr3:138488000-138519200	Weak transcription	Spleen	Spleen
36	chr3:138488200-138493000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:138488200-138493000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:138488200-138493200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:138488200-138493200	Weak transcription	Fetal Stomach	stomach
40	chr3:138488200-138494000	Weak transcription	Placenta	Placenta
41	chr3:138488200-138494000	Weak transcription	Fetal Thymus	thymus
42	chr3:138488200-138494200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:138488200-138494200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:138488200-138497000	Weak transcription	Fetal Intestine Large	intestine
45	chr3:138488200-138499600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:138488200-138499600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:138488200-138503200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:138488400-138493000	Weak transcription	A549	lung
49	chr3:138488400-138493000	Weak transcription	Hela-S3	cervix
50	chr3:138488400-138493400	Weak transcription	H1 Cell Line	embryonic stem cell

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