Variant report

Variant	rs1561458
Chromosome Location	chr15:44214169-44214170
allele	A/T
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	MAZ	chr15:44213971-44214908	IMR90	lung:	n/a	n/a
2	GATA3	chr15:44214064-44214662	MCF-7	breast:	n/a	n/a
3	CEBPB	chr15:44214147-44214594	IMR90	lung:	n/a	chr15:44214332-44214343
4	GATA3	chr15:44214111-44214766	SK-N-SH	brain:	n/a	chr15:44214686-44214696 chr15:44214688-44214698 chr15:44214689-44214696 chr15:44214682-44214703 chr15:44214689-44214696 chr15:44214689-44214696
5	ZNF263	chr15:44212818-44214261	HEK293-T-REx	kidney:	n/a	chr15:44213856-44213865
6	CEBPB	chr15:44214114-44214724	MCF-7	breast:	n/a	chr15:44214332-44214343
7	CEBPB	chr15:44214098-44214676	MCF-7	breast:	n/a	chr15:44214332-44214343
8	EP300	chr15:44214104-44214739	MCF-7	breast:	n/a	n/a
9	NR2F2	chr15:44214110-44214731	MCF-7	breast:	n/a	n/a
10	GATA3	chr15:44214085-44214864	MCF-7	breast:	n/a	chr15:44214686-44214696 chr15:44214688-44214698 chr15:44214689-44214696 chr15:44214682-44214703 chr15:44214689-44214696 chr15:44214689-44214696
11	GATA3	chr15:44213951-44214803	MCF-7	breast:	n/a	chr15:44214686-44214696 chr15:44214688-44214698 chr15:44214689-44214696 chr15:44214682-44214703 chr15:44214689-44214696 chr15:44214689-44214696
12	RCOR1	chr15:44213952-44214813	IMR90	lung:	n/a	n/a
13	TCF12	chr15:44213922-44214765	MCF-7	breast:	n/a	n/a
14	SIN3AK20	chr15:44213977-44214802	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:44209238..44212710-chr15:44213931..44216790,3	K562	blood:
2	chr15:44212995..44215958-chr15:44224697..44226821,2	K562	blood:
3	chr15:44213975..44214926-chr15:44267260..44268168,2	MCF-7	breast:

Variant related genes	Relation type
FRMD5	TF binding region
ENSG00000171877	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11853395	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16948098	1.00[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16949992	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2623015	0.85[EUR][1000 genomes]
rs28654093	1.00[EUR][1000 genomes]
rs28729677	0.83[EUR][1000 genomes]
rs2918952	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2929275	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2929277	0.83[EUR][1000 genomes]
rs2929279	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2929282	0.85[EUR][1000 genomes]
rs2930523	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2930524	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2930525	0.83[EUR][1000 genomes]
rs34497759	0.85[EUR][1000 genomes]
rs4270152	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4321171	1.00[EUR][1000 genomes]
rs481837	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs483800	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs492571	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs545119	0.97[EUR][1000 genomes]
rs56793082	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59561000	0.97[EUR][1000 genomes]
rs74009159	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74009160	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8035382	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs8035402	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs8035689	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
5	nsv1044435	chr15:44176103-44507403	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44196400-44216800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:44198200-44217600	Weak transcription	Brain Germinal Matrix	brain
3	chr15:44206800-44217800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:44207000-44214200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:44207200-44214600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:44208000-44217800	Weak transcription	NHLF	lung
7	chr15:44208800-44222600	Weak transcription	Fetal Brain Female	brain
8	chr15:44210800-44214400	Enhancers	HSMMtube	muscle
9	chr15:44211000-44214200	Enhancers	Fetal Muscle Leg	muscle
10	chr15:44211400-44214400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:44211600-44214200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr15:44211600-44214200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr15:44211600-44214400	Enhancers	Brain Substantia Nigra	brain
14	chr15:44211800-44214400	Enhancers	Fetal Heart	heart
15	chr15:44211800-44214600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:44211800-44221800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:44211800-44225000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:44212000-44214200	Enhancers	HSMM	muscle
19	chr15:44212200-44214800	Enhancers	Osteobl	bone
20	chr15:44212200-44215400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:44212400-44218000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr15:44212400-44220600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:44212400-44225000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:44212600-44218000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:44213000-44214400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:44213000-44214400	Weak transcription	Brain Anterior Caudate	brain
27	chr15:44213000-44214800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:44213000-44215600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:44213000-44217600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:44213200-44214200	Weak transcription	Fetal Brain Male	brain
31	chr15:44213200-44214400	Enhancers	Brain Hippocampus Middle	brain
32	chr15:44213200-44215400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr15:44213400-44214200	Enhancers	H9 Cell Line	embryonic stem cell
34	chr15:44213400-44217600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:44213400-44217800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:44213400-44217800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:44213400-44218400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr15:44213400-44221600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:44213600-44215600	Weak transcription	NH-A	brain
40	chr15:44213600-44216000	Weak transcription	Right Ventricle	heart
41	chr15:44213600-44217800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr15:44213600-44218000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr15:44213600-44219800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr15:44213800-44215200	Weak transcription	Brain Angular Gyrus	brain
45	chr15:44213800-44217600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr15:44213800-44217800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr15:44214000-44214200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:44214000-44214800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:44214000-44214800	Enhancers	HMEC	breast
50	chr15:44214000-44215000	Enhancers	NHEK	skin

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