Variant report

Variant	rs13071203
Chromosome Location	chr3:46733589-46733590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMARCB1	chr3:46733527-46735182	Hela-S3	cervix:	n/a	chr3:46733566-46733575 chr3:46734229-46734238

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:46732249..46733917-chr3:46887547..46889689,2	MCF-7	breast:
2	chr3:46728002..46730865-chr3:46732714..46734493,2	K562	blood:
3	chr3:46722742..46724325-chr3:46733459..46735116,2	K562	blood:
4	chr3:46727378..46730139-chr3:46733383..46735627,3	MCF-7	breast:
5	chr3:46724809..46726431-chr3:46731600..46733617,2	K562	blood:
6	chr3:46732167..46733968-chr3:46737534..46740232,2	MCF-7	breast:
7	chr3:46733350..46734890-chr3:46932280..46935238,2	MCF-7	breast:
8	chr3:46733050..46735013-chr3:46736523..46739104,3	K562	blood:
9	chr3:46589952..46592593-chr3:46732036..46734467,2	K562	blood:
10	chr3:46733404..46735141-chr3:46748725..46750536,2	MCF-7	breast:
11	chr3:46729365..46731831-chr3:46732714..46735067,2	K562	blood:

No data

Variant related genes	Relation type
ALS2CL	TF binding region
ENSG00000264306	Chromatin interaction
ENSG00000160801	Chromatin interaction
ENSG00000178038	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11718902	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719061	0.98[ASN][1000 genomes]
rs13073467	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683310	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683311	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9817508	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9847395	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9847407	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9849060	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9855064	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][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:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46705400-46734400	Weak transcription	Ovary	ovary
2	chr3:46717400-46733800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:46717800-46733600	Weak transcription	Brain Angular Gyrus	brain
4	chr3:46717800-46734000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:46720600-46733800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:46725600-46734000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:46727800-46734000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:46730000-46733800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:46730200-46734400	Weak transcription	Aorta	Aorta
10	chr3:46730800-46733800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:46731000-46733600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr3:46731000-46733600	Enhancers	Lung	lung
13	chr3:46731000-46734000	Enhancers	Adipose Nuclei	Adipose
14	chr3:46731200-46734000	Enhancers	Right Ventricle	heart
15	chr3:46731200-46734200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:46731400-46734000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:46731600-46733600	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr3:46731600-46734000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr3:46731600-46734000	Enhancers	Left Ventricle	heart
20	chr3:46731600-46734000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr3:46731600-46734200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:46731600-46734200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:46731800-46733600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr3:46731800-46733600	Enhancers	Duodenum Mucosa	Duodenum
25	chr3:46731800-46733800	Enhancers	Fetal Intestine Large	intestine
26	chr3:46731800-46734000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr3:46731800-46734200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr3:46732000-46733800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr3:46732000-46734200	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr3:46732000-46734200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:46732000-46734200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:46732000-46734200	Enhancers	Liver	Liver
33	chr3:46732000-46734200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr3:46732000-46734200	Enhancers	Placenta	Placenta
35	chr3:46732000-46734200	Enhancers	Right Atrium	heart
36	chr3:46732000-46734200	Enhancers	Stomach Mucosa	stomach
37	chr3:46732000-46734200	Flanking Active TSS	Hela-S3	cervix
38	chr3:46732000-46734200	Flanking Active TSS	NHEK	skin
39	chr3:46732000-46734400	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr3:46732200-46734200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr3:46732200-46734200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:46732200-46734400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:46732200-46734600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:46732600-46733800	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr3:46732600-46734000	Enhancers	Pancreas	Pancrea
46	chr3:46732600-46734000	Enhancers	A549	lung
47	chr3:46732600-46734600	Enhancers	Spleen	Spleen
48	chr3:46732800-46734000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr3:46732800-46734000	Weak transcription	Fetal Heart	heart
50	chr3:46733000-46733800	Enhancers	Skeletal Muscle Male	skeletal muscle

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