Variant report

Variant	rs2924787
Chromosome Location	chr15:100273422-100273423
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	CEBPD	chr15:100273374-100273693	HepG2	liver:	n/a	n/a
2	MAX	chr15:100273404-100274033	NB4	blood:	n/a	chr15:100273829-100273839
3	BACH1	chr15:100272807-100274184	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZKSCAN1	chr15:100273096-100273553	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr15:100273411-100274059	HCT-116	colon:	n/a	n/a
6	POLR2A	chr15:100273322-100274047	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr15:100272971-100274160	GM19193	blood:	n/a	n/a
8	POLR2A	chr15:100273362-100274249	HepG2	liver:	n/a	n/a
9	JUND	chr15:100273419-100273554	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr15:100273398-100273724	K562	blood:	n/a	n/a
11	POLR2A	chr15:100273290-100274388	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr15:100273366-100274125	A549	lung:	n/a	n/a
13	POLR2A	chr15:100273337-100274176	GM12892	blood:	n/a	n/a
14	POLR2A	chr15:100273248-100274078	ProgFib	skin:	n/a	n/a
15	MAX	chr15:100272976-100274106	MCF-7	breast:	n/a	chr15:100273829-100273839 chr15:100273091-100273101 chr15:100273030-100273039
16	MXI1	chr15:100272788-100274192	HepG2	liver:	n/a	n/a
17	POLR2A	chr15:100273209-100274111	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr15:100273376-100274068	GM10847	blood:	n/a	n/a
19	YY1	chr15:100273179-100274156	HepG2	liver:	n/a	n/a
20	POLR2A	chr15:100273361-100274216	PANC-1	pancreas:	n/a	n/a
21	PAX5	chr15:100273354-100273775	GM12892	blood:	n/a	n/a
22	CCNT2	chr15:100273066-100273777	K562	blood:	n/a	chr15:100273359-100273368
23	POLR2A	chr15:100273408-100274164	MCF10A-Er-Src	breast:	n/a	n/a
24	E2F6	chr15:100272795-100273478	A549	lung:	n/a	n/a
25	POLR2A	chr15:100273380-100273715	A549	lung:	n/a	n/a
26	POLR2A	chr15:100273308-100273707	ECC-1	luminal epithelium:	n/a	n/a
27	TCF3	chr15:100272936-100273643	GM12878	blood:	n/a	n/a
28	POLR2A	chr15:100273326-100274247	HUVEC	blood vessel:	n/a	n/a
29	SP1	chr15:100273309-100274194	A549	lung:	n/a	chr15:100273829-100273839 chr15:100273310-100273322 chr15:100273830-100273839 chr15:100274146-100274155 chr15:100273828-100273840 chr15:100273312-100273321 chr15:100273434-100273447 chr15:100273437-100273449 chr15:100273829-100273839 chr15:100273829-100273838 chr15:100273829-100273843 chr15:100273828-100273839 chr15:100273828-100273840 chr15:100273439-100273448 chr15:100274056-100274070 chr15:100273438-100273447 chr15:100273437-100273449
30	POLR2A	chr15:100273406-100273722	HepG2	liver:	n/a	n/a
31	POLR2A	chr15:100273342-100274225	H1-hESC	embryonic stem cell:	n/a	n/a
32	ZNF143	chr15:100273208-100273918	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr15:100273403-100273742	A549	lung:	n/a	n/a
34	POLR2A	chr15:100273361-100274145	GM12878	blood:	n/a	n/a
35	MAZ	chr15:100272245-100274211	IMR90	lung:	n/a	chr15:100273829-100273839 chr15:100273091-100273101 chr15:100273030-100273039
36	POLR2A	chr15:100273396-100273724	GM12878	blood:	n/a	n/a
37	PML	chr15:100273208-100274189	GM12878	blood:	n/a	n/a
38	ZBTB7A	chr15:100272759-100273801	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr15:100273349-100273723	PANC-1	pancreas:	n/a	n/a
40	MAX	chr15:100273059-100273647	HepG2	liver:	n/a	chr15:100273091-100273101
41	MAZ	chr15:100272890-100274127	Hela-S3	cervix:	n/a	chr15:100273829-100273839 chr15:100273091-100273101 chr15:100273030-100273039
42	POLR2A	chr15:100273338-100273736	K562	blood:	n/a	n/a
43	SP1	chr15:100273380-100274126	A549	lung:	n/a	chr15:100273829-100273839 chr15:100273830-100273839 chr15:100273828-100273840 chr15:100273434-100273447 chr15:100273437-100273449 chr15:100273829-100273839 chr15:100273829-100273838 chr15:100273829-100273843 chr15:100273828-100273839 chr15:100273828-100273840 chr15:100273439-100273448 chr15:100274056-100274070 chr15:100273438-100273447 chr15:100273437-100273449
44	POLR2A	chr15:100273373-100274063	K562	blood:	n/a	n/a
45	ELF1	chr15:100273214-100274224	GM12878	blood:	n/a	chr15:100273809-100273822 chr15:100273811-100273822 chr15:100273811-100273822 chr15:100273812-100273821
46	RUNX3	chr15:100273219-100273764	GM12878	blood:	n/a	n/a
47	CEBPB	chr15:100273327-100274082	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr15:100273408-100273646	HepG2	liver:	n/a	n/a
49	POLR2A	chr15:100273371-100274118	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr15:100273384-100273691	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:100257917..100259969-chr15:100273281..100275251,2	MCF-7	breast:
2	chr15:99826798..99828339-chr15:100272977..100274878,2	MCF-7	breast:
3	chr15:99789846..99791808-chr15:100272487..100274799,2	MCF-7	breast:
4	chr15:100105670..100107207-chr15:100272767..100275061,2	MCF-7	breast:

Variant related genes	Relation type
LYSMD4	TF binding region
ENSG00000068305	Chromatin interaction
ENSG00000168904	Chromatin interaction
ENSG00000214397	Chromatin interaction
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 8 )

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1038005	chr15:100170414-100633714	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv542522	chr15:100170414-100633714	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv904560	chr15:100196657-100339331	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
7	nsv904561	chr15:100204918-100486828	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv428313	chr15:100236203-100757039	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
9	nsv904563	chr15:100239546-100274747	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv570730	chr15:100240910-100700520	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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
11	nsv1045838	chr15:100243067-101032218	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv904564	chr15:100245296-100723798	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats 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
13	nsv932678	chr15:100250311-101012358	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
14	esv3356054	chr15:100272454-100275002	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2924787	LYSMD4	cis	Thyroid	GTEx
rs2924787	LYSMD4	cis	putamen	BrainEAC
rs2924787	LYSMD4	cis	hippocampus	BrainEAC
rs2924787	LYSMD4	cis	inferior olivary nucleus	BrainEAC
rs2924787	LYSMD4	cis	frontal cortex	BrainEAC
rs2924787	LYSMD4	cis	brain	BrainEAC
rs2924787	LYSMD4	cis	cerebellar cortex	BrainEAC
rs2924787	LYSMD4	cis	intralobular white matter	BrainEAC

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100271200-100274000	Active TSS	Fetal Intestine Large	intestine
2	chr15:100271600-100274200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr15:100271800-100274200	Active TSS	Rectal Smooth Muscle	rectum
4	chr15:100272000-100273600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr15:100272000-100274000	Active TSS	Colon Smooth Muscle	Colon
6	chr15:100272000-100274000	Active TSS	Fetal Intestine Small	intestine
7	chr15:100272000-100274200	Active TSS	NHLF	lung
8	chr15:100272200-100274000	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr15:100272200-100274000	Active TSS	Fetal Stomach	stomach
10	chr15:100272200-100274000	Active TSS	Right Atrium	heart
11	chr15:100272200-100274000	Active TSS	Right Ventricle	heart
12	chr15:100272200-100274200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:100272200-100274200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:100272200-100274200	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr15:100272400-100274000	Active TSS	Muscle Satellite Cultured Cells	--
16	chr15:100272400-100274000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:100272400-100274000	Active TSS	Left Ventricle	heart
18	chr15:100272400-100274000	Active TSS	Lung	lung
19	chr15:100272400-100274000	Active TSS	Pancreas	Pancrea
20	chr15:100272400-100274000	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr15:100272400-100274200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:100272400-100274200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:100272400-100274200	Active TSS	Aorta	Aorta
24	chr15:100272400-100274200	Active TSS	Esophagus	oesophagus
25	chr15:100272400-100274200	Active TSS	Fetal Kidney	kidney
26	chr15:100272400-100274200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr15:100272400-100274200	Active TSS	Ovary	ovary
28	chr15:100272400-100274200	Active TSS	NHDF-Ad	bronchial
29	chr15:100272400-100274400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:100272600-100273600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:100272600-100273600	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr15:100272600-100274000	Active TSS	Brain Cingulate Gyrus	brain
33	chr15:100272600-100274000	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr15:100272600-100274200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:100272600-100274200	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr15:100272600-100274400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:100272800-100274000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:100272800-100274000	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr15:100272800-100274000	Active TSS	Brain Angular Gyrus	brain
40	chr15:100272800-100274000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:100272800-100274000	Active TSS	Duodenum Mucosa	Duodenum
42	chr15:100272800-100274000	Active TSS	Fetal Heart	heart
43	chr15:100272800-100274000	Active TSS	Gastric	stomach
44	chr15:100272800-100274000	Active TSS	Stomach Mucosa	stomach
45	chr15:100272800-100274000	Active TSS	A549	lung
46	chr15:100272800-100274000	Active TSS	Osteobl	bone
47	chr15:100272800-100274200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:100272800-100274200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:100272800-100274200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:100272800-100274200	Active TSS	Brain Germinal Matrix	brain

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