Variant report

Variant	rs12440103
Chromosome Location	chr15:56036068-56036069
allele	A/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	GATA2	chr15:56035216-56036671	SH-SY5Y	brain:	n/a	n/a
2	TCF12	chr15:56034098-56036186	A549	lung:	n/a	chr15:56034864-56034871 chr15:56036136-56036146
3	MXI1	chr15:56032346-56036713	SK-N-SH	brain:	n/a	chr15:56034632-56034641
4	GATA3	chr15:56036015-56036422	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:56035905..56037422-chr15:56138325..56141165,2	MCF-7	breast:
2	chr15:56033858..56036761-chr15:56051440..56053715,2	MCF-7	breast:
3	chr15:56035867..56037850-chr15:56069521..56071241,2	MCF-7	breast:
4	chr15:56034248..56036795-chr15:56038057..56039658,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259369	TF binding region
PRTG	TF binding region
ENSG00000259369	Chromatin interaction
ENSG00000221218	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1011061	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152116	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152830	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851590	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071203	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071204	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11632579	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11632762	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11639086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852746	1.00[ASN][1000 genomes]
rs11853533	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855737	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11857254	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857271	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438264	0.83[AFR][1000 genomes]
rs12438394	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439011	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442165	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899647	1.00[ASN][1000 genomes]
rs12899976	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901963	1.00[ASN][1000 genomes]
rs12903239	1.00[ASN][1000 genomes]
rs12905693	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906885	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907557	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907772	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907892	1.00[ASN][1000 genomes]
rs12908232	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908813	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910180	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911682	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912118	0.90[ASN][1000 genomes]
rs12914863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915092	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12915423	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34303822	1.00[ASN][1000 genomes]
rs3985768	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412917	1.00[ASN][1000 genomes]
rs4774222	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55874929	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66519039	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028880	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
5	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv1052495	chr15:56013617-56102164	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3390617	chr15:56034285-56036833	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56031400-56036600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:56032600-56036200	Active TSS	Fetal Kidney	kidney
3	chr15:56033400-56036200	Active TSS	Ovary	ovary
4	chr15:56033600-56036200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
5	chr15:56034000-56036200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
6	chr15:56034200-56036200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr15:56034200-56036200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
8	chr15:56034200-56036200	Active TSS	Fetal Lung	lung
9	chr15:56034400-56036200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr15:56034400-56036200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:56034400-56036200	Active TSS	Brain Substantia Nigra	brain
12	chr15:56034400-56036400	Active TSS	Stomach Smooth Muscle	stomach
13	chr15:56034400-56036600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr15:56034600-56036200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr15:56034600-56036200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:56034600-56036200	Active TSS	Muscle Satellite Cultured Cells	--
17	chr15:56034600-56036200	Active TSS	Brain Anterior Caudate	brain
18	chr15:56034600-56036200	Active TSS	Brain Cingulate Gyrus	brain
19	chr15:56034600-56036200	Active TSS	HepG2	liver
20	chr15:56034600-56036400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr15:56034600-56036400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:56034600-56036400	Active TSS	Rectal Smooth Muscle	rectum
23	chr15:56034600-56036600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:56034800-56036200	Active TSS	Brain Angular Gyrus	brain
25	chr15:56034800-56036200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
26	chr15:56035000-56036600	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr15:56035400-56036200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:56035400-56036200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
29	chr15:56035600-56036200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
30	chr15:56035600-56036200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:56035600-56036200	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
32	chr15:56035600-56036200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
33	chr15:56035600-56036400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:56035800-56036200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
35	chr15:56035800-56036200	Active TSS	Primary hematopoietic stem cells	blood
36	chr15:56035800-56036200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:56035800-56036200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr15:56035800-56036200	Flanking Active TSS	Fetal Intestine Large	intestine
39	chr15:56035800-56036200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
40	chr15:56035800-56036200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
41	chr15:56035800-56036200	Flanking Active TSS	HUVEC	blood vessel
42	chr15:56035800-56036200	Flanking Active TSS	NHLF	lung
43	chr15:56035800-56036200	Flanking Bivalent TSS/Enh	Osteobl	bone
44	chr15:56035800-56036400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr15:56035800-56036400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:56035800-56036400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr15:56035800-56036400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:56036000-56036200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:56036000-56036200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr15:56036000-56036200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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