Variant report

Variant	rs56745438
Chromosome Location	chr15:99792334-99792335
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	chr15:99790318-99793089	GM12891	blood:	n/a	n/a
2	ELK1	chr15:99790867-99792338	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:99792277-99792415	HepG2	liver:	n/a	n/a
4	MXI1	chr15:99790979-99792430	Hela-S3	cervix:	n/a	n/a
5	ARID3A	chr15:99791850-99792363	K562	blood:	n/a	n/a
6	BRCA1	chr15:99792106-99792525	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr15:99791037-99792538	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:99789370-99792567	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr15:99791797-99792492	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr15:99789544-99792397	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr15:99790665-99792519	PBDE	blood:	n/a	n/a
12	MAX	chr15:99790822-99792339	Hela-S3	cervix:	n/a	chr15:99791567-99791577
13	HCFC1	chr15:99788182-99792843	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:99643812..99646594-chr15:99789555..99792592,4	MCF-7	breast:
2	chr15:99788127..99791108-chr15:99792243..99793962,2	K562	blood:
3	chr15:99788657..99793033-chr15:100273651..100276844,5	MCF-7	breast:
4	chr15:99790531..99793156-chr15:100244093..100247016,2	MCF-7	breast:

Variant related genes	Relation type
TTC23	TF binding region
ENSG00000183060	Chromatin interaction
ENSG00000103852	Chromatin interaction
ENSG00000259475	Chromatin interaction
ENSG00000068305	Chromatin interaction
ENSG00000182253	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs55962871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57439349	1.00[AMR][1000 genomes]
rs57466507	1.00[AMR][1000 genomes]
rs57791697	1.00[AMR][1000 genomes]
rs58475408	1.00[AMR][1000 genomes]
rs58905808	1.00[AMR][1000 genomes]
rs60517250	1.00[AMR][1000 genomes]
rs60899471	1.00[AMR][1000 genomes]
rs61034773	1.00[AMR][1000 genomes]
rs61452337	1.00[AMR][1000 genomes]
rs7166159	1.00[AMR][1000 genomes]
rs73463351	1.00[AMR][1000 genomes]
rs73463357	1.00[AMR][1000 genomes]
rs73471380	1.00[AMR][1000 genomes]
rs73473367	1.00[AMR][1000 genomes]
rs73473382	1.00[AMR][1000 genomes]
rs73473383	1.00[AMR][1000 genomes]
rs73473394	1.00[AMR][1000 genomes]
rs73473399	1.00[AMR][1000 genomes]
rs73475311	1.00[AMR][1000 genomes]
rs73475313	1.00[AMR][1000 genomes]
rs73476348	1.00[AMR][1000 genomes]
rs73476350	1.00[AMR][1000 genomes]
rs73482318	1.00[AMR][1000 genomes]
rs74033465	1.00[AMR][1000 genomes]
rs74033470	1.00[AMR][1000 genomes]
rs74033471	1.00[AMR][1000 genomes]
rs74033474	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS 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	60 gene(s)	inside rSNPs	diseases
4	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
10	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
13	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
14	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
16	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
17	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
19	nsv1045367	chr15:99781626-99892182	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99787400-99792400	Active TSS	GM12878-XiMat	blood
2	chr15:99788200-99792400	Active TSS	Aorta	Aorta
3	chr15:99788200-99792400	Active TSS	Fetal Intestine Small	intestine
4	chr15:99788200-99792600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:99788400-99792400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr15:99788400-99792600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:99788400-99792600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr15:99788400-99792600	Active TSS	Fetal Intestine Large	intestine
9	chr15:99788400-99792600	Active TSS	Right Ventricle	heart
10	chr15:99788400-99792800	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr15:99788400-99792800	Active TSS	HSMMtube	muscle
12	chr15:99788600-99792400	Active TSS	H1 Cell Line	embryonic stem cell
13	chr15:99788600-99792400	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr15:99788600-99792400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:99788600-99792400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:99788600-99792400	Active TSS	Colonic Mucosa	Colon
17	chr15:99788600-99792400	Active TSS	Fetal Kidney	kidney
18	chr15:99788600-99792600	Active TSS	Fetal Muscle Trunk	muscle
19	chr15:99788600-99792800	Active TSS	H9 Cell Line	embryonic stem cell
20	chr15:99788800-99792400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:99788800-99792400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:99788800-99792400	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr15:99788800-99792400	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr15:99788800-99792400	Active TSS	HMEC	breast
25	chr15:99788800-99792400	Active TSS	NHEK	skin
26	chr15:99788800-99792800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:99788800-99792800	Active TSS	Fetal Stomach	stomach
28	chr15:99789000-99792400	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr15:99789000-99792400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:99789000-99792400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:99789000-99792400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:99789000-99792400	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr15:99789000-99792400	Active TSS	Fetal Muscle Leg	muscle
34	chr15:99789000-99792400	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr15:99789000-99792400	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr15:99789000-99792400	Active TSS	A549	lung
37	chr15:99789000-99792400	Active TSS	HSMM	muscle
38	chr15:99789000-99792400	Active TSS	NHDF-Ad	bronchial
39	chr15:99789000-99792600	Active TSS	Psoas Muscle	Psoas
40	chr15:99789200-99792400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr15:99789200-99792400	Active TSS	Brain Anterior Caudate	brain
42	chr15:99789200-99792400	Active TSS	Placenta	Placenta
43	chr15:99789200-99792400	Active TSS	Fetal Thymus	thymus
44	chr15:99789200-99792400	Active TSS	NH-A	brain
45	chr15:99789400-99792400	Active TSS	Brain Angular Gyrus	brain
46	chr15:99789400-99792400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:99789400-99792600	Active TSS	Stomach Mucosa	stomach
48	chr15:99789400-99792600	Active TSS	Thymus	Thymus
49	chr15:99789600-99792800	Active TSS	Brain Germinal Matrix	brain
50	chr15:99789600-99792800	Active TSS	K562	blood

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