Variant report

Variant	rs72899356
Chromosome Location	chr3:46732059-46732060
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr3:46732027-46732712	ECC-1	luminal epithelium:	n/a	n/a
2	HCFC1	chr3:46731998-46732740	Hela-S3	cervix:	n/a	n/a
3	NFIC	chr3:46732022-46732808	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:46730164..46732483-chr3:46734488..46736983,2	MCF-7	breast:
2	chr3:46711657..46716189-chr3:46730133..46733448,4	MCF-7	breast:
3	chr3:46724809..46726431-chr3:46731600..46733617,2	K562	blood:
4	chr3:46589952..46592593-chr3:46732036..46734467,2	K562	blood:

No data

Variant related genes	Relation type
ALS2CL	TF binding region
ENSG00000264306	Chromatin interaction
ENSG00000178038	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs59661801	1.00[AFR][1000 genomes]
rs72892141	1.00[AFR][1000 genomes]
rs72892151	1.00[AFR][1000 genomes]
rs72899352	1.00[AFR][1000 genomes]
rs72899357	1.00[AFR][1000 genomes]
rs72899360	1.00[AFR][1000 genomes]
rs72899363	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv876739	chr3:46656980-46744966	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv876740	chr3:46656980-46748453	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv876741	chr3:46663372-46763839	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv516623	chr3:46680063-46852679	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	esv1804680	chr3:46704348-46869911	Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv876742	chr3:46705369-46763839	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
11	nsv536555	chr3:46706571-46817963	Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv536556	chr3:46706571-46849443	Genic enhancers Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv536557	chr3:46706571-46853434	Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
15	nsv10268	chr3:46707169-46736718	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
16	esv1797503	chr3:46708712-46760713	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
17	nsv876743	chr3:46716523-46753577	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
18	nsv876744	chr3:46716523-46763839	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
19	nsv460525	chr3:46728659-46790397	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
20	nsv590179	chr3:46728659-46790397	Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
21	esv1847964	chr3:46729757-46753976	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46702800-46732400	Weak transcription	Psoas Muscle	Psoas
2	chr3:46705400-46732600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:46705400-46734400	Weak transcription	Ovary	ovary
4	chr3:46717400-46733800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:46717800-46733600	Weak transcription	Brain Angular Gyrus	brain
6	chr3:46717800-46734000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:46720600-46733800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:46724200-46732200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr3:46725600-46734000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:46727800-46732200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:46727800-46732400	Weak transcription	Thymus	Thymus
12	chr3:46727800-46734000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:46728600-46732200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:46729800-46732800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:46730000-46733800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:46730200-46732600	Weak transcription	Gastric	stomach
17	chr3:46730200-46734400	Weak transcription	Aorta	Aorta
18	chr3:46730800-46733800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:46731000-46732200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr3:46731000-46732200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:46731000-46732600	Weak transcription	Pancreas	Pancrea
22	chr3:46731000-46733600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr3:46731000-46733600	Enhancers	Lung	lung
24	chr3:46731000-46734000	Enhancers	Adipose Nuclei	Adipose
25	chr3:46731200-46732600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr3:46731200-46734000	Enhancers	Right Ventricle	heart
27	chr3:46731200-46734200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:46731400-46732200	Enhancers	Primary T cells fromperipheralblood	blood
29	chr3:46731400-46733400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr3:46731400-46734000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:46731600-46732400	Enhancers	Primary T cells from cord blood	blood
32	chr3:46731600-46733600	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr3:46731600-46734000	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr3:46731600-46734000	Enhancers	Left Ventricle	heart
35	chr3:46731600-46734000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr3:46731600-46734200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:46731600-46734200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:46731800-46732200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:46731800-46732200	Enhancers	HMEC	breast
40	chr3:46731800-46732800	Enhancers	Fetal Heart	heart
41	chr3:46731800-46733000	Enhancers	Colonic Mucosa	Colon
42	chr3:46731800-46733600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr3:46731800-46733600	Enhancers	Duodenum Mucosa	Duodenum
44	chr3:46731800-46733800	Enhancers	Fetal Intestine Large	intestine
45	chr3:46731800-46734000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr3:46731800-46734200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr3:46732000-46732200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:46732000-46732200	Enhancers	Brain Hippocampus Middle	brain
49	chr3:46732000-46732200	Flanking Active TSS	Spleen	Spleen
50	chr3:46732000-46732800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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