Variant report

Variant	rs57867560
Chromosome Location	chr15:78440360-78440361
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:78440163-78440983	GM12892	blood:	n/a	n/a
2	POLR2A	chr15:78440290-78440572	MCF-7	breast:	n/a	n/a
3	POLR2A	chr15:78440295-78442601	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:78440117-78442262	GM18505	blood:	n/a	n/a
5	POLR2A	chr15:78440139-78441984	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:78440255-78440861	K562	blood:	n/a	n/a
7	MTA3	chr15:78440192-78440829	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:78439724-78440745	K562	blood:	n/a	n/a
9	POLR2A	chr15:78440062-78441950	GM12891	blood:	n/a	n/a
10	POLR2A	chr15:78440063-78440916	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:78438626..78440576-chr15:78459614..78461953,2	K562	blood:
2	chr15:78414752..78417603-chr15:78438939..78440752,2	MCF-7	breast:
3	chr15:78421103..78425437-chr15:78438436..78443517,9	MCF-7	breast:
4	chr15:78439170..78443635-chr15:78452310..78455814,4	K562	blood:
5	chr15:78440356..78444633-chr15:78445807..78449726,8	K562	blood:
6	chr15:78422180..78427678-chr15:78438636..78444300,13	MCF-7	breast:
7	chr15:78422233..78425731-chr15:78438987..78443227,7	K562	blood:
8	chr15:78433535..78435923-chr15:78440184..78443056,4	K562	blood:
9	chr15:78437651..78440580-chr15:78459542..78461046,2	MCF-7	breast:
10	chr15:78422015..78425228-chr15:78439030..78443289,7	K562	blood:

No data

Variant related genes	Relation type
IDH3A	TF binding region
ENSG00000166411	Chromatin interaction
ENSG00000136425	Chromatin interaction
ENSG00000260988	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11854120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856106	0.94[ASN][1000 genomes]
rs17479031	1.00[ASN][1000 genomes]
rs17479135	1.00[ASN][1000 genomes]
rs17850483	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17850484	1.00[ASN][1000 genomes]
rs3825847	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4570804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009331	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62009333	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009334	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009336	0.92[EUR][1000 genomes]
rs62009337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009341	0.92[EUR][1000 genomes]
rs62009342	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009343	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009347	0.82[EUR][1000 genomes]
rs62009348	0.82[EUR][1000 genomes]
rs7165154	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS 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 miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv948437	chr15:78435527-78504662	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS 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	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78424600-78440800	Weak transcription	HSMMtube	muscle
2	chr15:78425000-78440600	Weak transcription	Fetal Stomach	stomach
3	chr15:78433000-78440600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:78433600-78440400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:78435200-78440400	Weak transcription	HepG2	liver
6	chr15:78436000-78440600	Weak transcription	Thymus	Thymus
7	chr15:78437600-78440600	Weak transcription	HSMM	muscle
8	chr15:78438200-78441000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:78438400-78440400	Weak transcription	Liver	Liver
10	chr15:78438400-78440800	Enhancers	Adipose Nuclei	Adipose
11	chr15:78438400-78440800	Enhancers	Fetal Intestine Large	intestine
12	chr15:78438400-78441000	Enhancers	Psoas Muscle	Psoas
13	chr15:78438600-78440600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:78438600-78440600	Enhancers	Hela-S3	cervix
15	chr15:78438600-78440600	Enhancers	NHEK	skin
16	chr15:78438600-78440800	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr15:78438600-78441000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr15:78438600-78441000	Enhancers	Placenta	Placenta
19	chr15:78438800-78440400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:78438800-78440600	Enhancers	K562	blood
21	chr15:78438800-78440800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:78438800-78440800	Enhancers	HMEC	breast
23	chr15:78438800-78441000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:78438800-78441200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:78439000-78440400	Enhancers	A549	lung
26	chr15:78439000-78440600	Weak transcription	NHDF-Ad	bronchial
27	chr15:78439000-78440800	Enhancers	Esophagus	oesophagus
28	chr15:78439000-78440800	Enhancers	Fetal Heart	heart
29	chr15:78439000-78440800	Enhancers	Pancreas	Pancrea
30	chr15:78439200-78440400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:78439200-78441000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr15:78439400-78440400	Weak transcription	Osteobl	bone
33	chr15:78439400-78440600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr15:78439800-78440400	Enhancers	Left Ventricle	heart
35	chr15:78439800-78440600	Enhancers	Duodenum Mucosa	Duodenum
36	chr15:78439800-78440600	Enhancers	Placenta Amnion	Placenta Amnion
37	chr15:78439800-78440800	Enhancers	Stomach Mucosa	stomach
38	chr15:78440000-78440400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr15:78440000-78440800	Enhancers	Fetal Intestine Small	intestine
40	chr15:78440000-78440800	Enhancers	Fetal Muscle Leg	muscle
41	chr15:78440000-78440800	Enhancers	Lung	lung
42	chr15:78440000-78440800	Enhancers	Right Atrium	heart
43	chr15:78440000-78441000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:78440000-78441000	Enhancers	Spleen	Spleen
45	chr15:78440200-78440400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:78440200-78440400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:78440200-78440400	Enhancers	GM12878-XiMat	blood
48	chr15:78440200-78440600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:78440200-78440600	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr15:78440200-78440600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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