Variant report

Variant	rs12438394
Chromosome Location	chr15:56033847-56033848
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	KAP1	chr15:56032743-56034052	HEK293	kidney:	n/a	n/a
2	SMARCB1	chr15:56033753-56036042	Hela-S3	cervix:	n/a	n/a
3	KAP1	chr15:56033047-56034093	U2OS	brain:	n/a	n/a
4	POLR2A	chr15:56033776-56035901	HepG2	liver:	n/a	n/a
5	ZNF143	chr15:56033821-56034134	H1-hESC	embryonic stem cell:	n/a	n/a
6	MXI1	chr15:56032346-56036713	SK-N-SH	brain:	n/a	chr15:56034632-56034641
7	POLR2A	chr15:56033732-56035727	Hela-S3	cervix:	n/a	n/a
8	TCF7L2	chr15:56032947-56034128	HEK293	kidney:	n/a	chr15:56034066-56034075 chr15:56034067-56034077 chr15:56034064-56034078
9	TCF7L2	chr15:56033793-56035428	Hela-S3	cervix:	n/a	chr15:56034066-56034075 chr15:56034067-56034077 chr15:56034064-56034078 chr15:56034196-56034210
10	CEBPB	chr15:56033840-56034116	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:55965960..55968011-chr15:56032220..56035162,2	MCF-7	breast:
2	chr15:56033073..56035225-chr17:56708615..56710685,2	MCF-7	breast:
3	chr15:56031905..56035384-chr15:56036677..56038977,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259369	TF binding region
ENSG00000259369	Chromatin interaction
ENSG00000166450	Chromatin interaction
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1011061	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152116	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152830	0.95[AMR][1000 genomes];0.97[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	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071204	0.93[AMR][1000 genomes];0.94[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	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852746	1.00[ASN][1000 genomes]
rs11853533	0.93[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	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857271	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439011	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440103	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442165	0.89[AMR][1000 genomes];0.93[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906885	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907557	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907772	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907892	1.00[ASN][1000 genomes]
rs12908232	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908813	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910180	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911682	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912118	0.90[ASN][1000 genomes]
rs12914863	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915092	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12915423	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34303822	1.00[ASN][1000 genomes]
rs3985768	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412917	1.00[ASN][1000 genomes]
rs4774222	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55874929	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66519039	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028880	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56030400-56034600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:56030600-56034600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:56031200-56034200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:56031400-56036600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:56032200-56034200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr15:56032400-56034200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr15:56032600-56034200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
8	chr15:56032600-56035400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:56032600-56036200	Active TSS	Fetal Kidney	kidney
10	chr15:56032800-56034000	Active TSS	Stomach Smooth Muscle	stomach
11	chr15:56033000-56034800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:56033200-56034000	Flanking Active TSS	A549	lung
13	chr15:56033200-56034200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
14	chr15:56033200-56034400	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
15	chr15:56033200-56034600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:56033200-56036000	Active TSS	Placenta Amnion	Placenta Amnion
17	chr15:56033400-56034000	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
18	chr15:56033400-56034000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
19	chr15:56033400-56034000	Flanking Active TSS	HepG2	liver
20	chr15:56033400-56034200	Bivalent/Poised TSS	Fetal Brain Female	brain
21	chr15:56033400-56034400	Flanking Active TSS	Hela-S3	cervix
22	chr15:56033400-56034600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
23	chr15:56033400-56036200	Active TSS	Ovary	ovary
24	chr15:56033600-56034000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
25	chr15:56033600-56034000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:56033600-56034000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:56033600-56034000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
28	chr15:56033600-56034000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:56033600-56034000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
30	chr15:56033600-56034000	Flanking Active TSS	Placenta	Placenta
31	chr15:56033600-56034200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr15:56033600-56034200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
33	chr15:56033600-56034200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
34	chr15:56033600-56034200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
35	chr15:56033600-56034200	Bivalent Enhancer	Fetal Heart	heart
36	chr15:56033600-56034200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
37	chr15:56033600-56034400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
38	chr15:56033600-56034400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
39	chr15:56033600-56034400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
40	chr15:56033600-56034400	Bivalent Enhancer	Liver	Liver
41	chr15:56033600-56034400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr15:56033600-56034400	Flanking Active TSS	HSMM	muscle
43	chr15:56033600-56034600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
44	chr15:56033600-56034600	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr15:56033600-56034600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr15:56033600-56034600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:56033600-56034600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
48	chr15:56033600-56034600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
49	chr15:56033600-56034600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:56033600-56034600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle

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