Variant report

Variant	rs8030331
Chromosome Location	chr15:100274144-100274145
allele	C/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	BACH1	chr15:100272807-100274184	H1-hESC	embryonic stem cell:	n/a	n/a
2	RCOR1	chr15:100273615-100274281	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:100272971-100274160	GM19193	blood:	n/a	n/a
4	POLR2A	chr15:100273362-100274249	HepG2	liver:	n/a	n/a
5	POLR2A	chr15:100273290-100274388	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr15:100273337-100274176	GM12892	blood:	n/a	n/a
7	MXI1	chr15:100272788-100274192	HepG2	liver:	n/a	n/a
8	STAT3	chr15:100273947-100274227	GM12878	blood:	n/a	chr15:100274057-100274069
9	YY1	chr15:100273179-100274156	HepG2	liver:	n/a	n/a
10	POLR2A	chr15:100273361-100274216	PANC-1	pancreas:	n/a	n/a
11	ELF1	chr15:100273589-100274277	MCF-7	breast:	n/a	chr15:100273809-100273822 chr15:100273811-100273822 chr15:100273811-100273822 chr15:100273812-100273821
12	POLR2A	chr15:100273408-100274164	MCF10A-Er-Src	breast:	n/a	n/a
13	SMC3	chr15:100273889-100274189	GM12878	blood:	n/a	n/a
14	TAF1	chr15:100273648-100274176	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr15:100273326-100274247	HUVEC	blood vessel:	n/a	n/a
16	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
17	POLR2A	chr15:100273342-100274225	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr15:100273361-100274145	GM12878	blood:	n/a	n/a
19	MAZ	chr15:100272245-100274211	IMR90	lung:	n/a	chr15:100273829-100273839 chr15:100273091-100273101 chr15:100273030-100273039
20	ELF1	chr15:100273522-100274155	MCF-7	breast:	n/a	chr15:100273809-100273822 chr15:100273811-100273822 chr15:100273811-100273822 chr15:100273812-100273821
21	PML	chr15:100273208-100274189	GM12878	blood:	n/a	n/a
22	ELF1	chr15:100273214-100274224	GM12878	blood:	n/a	chr15:100273809-100273822 chr15:100273811-100273822 chr15:100273811-100273822 chr15:100273812-100273821
23	MTA3	chr15:100273712-100274205	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:100273330-100274181	HEK293	kidney:	n/a	n/a
25	MAZ	chr15:100273387-100274190	GM12878	blood:	n/a	chr15:100273829-100273839
26	CHD2	chr15:100272844-100274197	H1-hESC	embryonic stem cell:	n/a	chr15:100273093-100273103
27	MAX	chr15:100273825-100274222	GM12878	blood:	n/a	chr15:100273829-100273839
28	POLR2A	chr15:100273384-100274172	HL-60	blood:	n/a	n/a
29	POLR2A	chr15:100273102-100274179	GM18526	blood:	n/a	n/a
30	SP1	chr15:100273499-100274188	H1-hESC	embryonic stem cell:	n/a	chr15:100273829-100273839 chr15:100273830-100273839 chr15:100274146-100274155 chr15:100273828-100273840 chr15:100273829-100273839 chr15:100273829-100273838 chr15:100273829-100273843 chr15:100273828-100273839 chr15:100273828-100273840 chr15:100274056-100274070
31	CHD2	chr15:100273353-100274171	GM12878	blood:	n/a	n/a
32	CREB1	chr15:100273061-100274304	HepG2	liver:	n/a	n/a
33	POLR2A	chr15:100273236-100274225	PBDE	blood:	n/a	n/a
34	SIN3AK20	chr15:100273289-100274359	MCF-7	breast:	n/a	n/a
35	POLR2A	chr15:100273303-100274154	MCF-7	breast:	n/a	n/a
36	POLR2A	chr15:100273372-100274180	K562	blood:	n/a	n/a
37	POLR2A	chr15:100272902-100274233	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr15:100273715-100274144	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr15:100273410-100274148	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr15:100273459-100274148	GM12878	blood:	n/a	n/a
41	POLR2A	chr15:100273346-100274170	NB4	blood:	n/a	n/a
42	POLR2A	chr15:100273254-100274167	GM18951	blood:	n/a	n/a
43	ZBTB7A	chr15:100273876-100274294	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr15:100273773-100274145	HepG2	liver:	n/a	n/a
45	FOXM1	chr15:100273765-100274147	GM12878	blood:	n/a	n/a
46	TCF12	chr15:100273612-100274248	A549	lung:	n/a	n/a
47	PML	chr15:100273405-100274235	MCF-7	breast:	n/a	n/a
48	HEY1	chr15:100273255-100274199	HepG2	liver:	n/a	chr15:100273829-100273844
49	CEBPD	chr15:100273801-100274156	HepG2	liver:	n/a	n/a
50	MAX	chr15:100272719-100274219	A549	lung:	n/a	chr15:100273829-100273839 chr15:100273091-100273101 chr15:100273030-100273039

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:100274128-100274178	HRCEpiC	kidney:	n/a
2	chr15:100274128-100274178	HCT-116	colon:	n/a
3	chr15:100274128-100274178	T-47D	breast:	n/a
4	chr15:100274128-100274178	HAEpiC	amniotic membrane:	n/a
5	chr15:100274128-100274178	HRE	kidney:	n/a
6	chr15:100274128-100274178	AG09319	gingival:	n/a
7	chr15:100274128-100274178	ovcar-3	ovarian:	n/a
8	chr15:100274128-100274178	AG04449	skin:	fetal
9	chr15:100274128-100274178	SK-N-MC	brain:	n/a
10	chr15:100274128-100274178	AoSMC	blood vessel:	n/a
11	chr15:100274128-100274178	HL-60	blood:	n/a
12	chr15:100274128-100274178	HCPEpiC	choroid plexus:	n/a
13	chr15:100274128-100274178	K562	blood:	n/a
14	chr15:100274128-100274178	CMK	blood:	n/a
15	chr15:100274128-100274178	SKMC	muscle:	n/a
16	chr15:100274128-100274178	MCF-7	breast:	n/a
17	chr15:100274128-100274178	NB4	blood:	n/a
18	chr15:100274128-100274178	HCM	heart:	n/a
19	chr15:100274128-100274178	RPTEC	kidney:	n/a
20	chr15:100274128-100274178	ProgFib	skin:	n/a
21	chr15:100274128-100274178	SAEC	small airway:	n/a
22	chr15:100274128-100274178	HMEC	breast:	n/a
23	chr15:100274128-100274178	GM06990	blood:	n/a
24	chr15:100274128-100274178	NHBE	bronchial:	n/a
25	chr15:100274128-100274178	PrEC	prostate:	n/a
26	chr15:100274128-100274178	Jurkat	blood:	n/a
27	chr15:100274128-100274178	HEEpiC	esophagus:	n/a
28	chr15:100274128-100274178	MCF10A-Er-Src	breast:	n/a
29	chr15:100274128-100274178	HNPCEpiC	eye:	n/a
30	chr15:100274128-100274178	Caco-2	colon:	n/a
31	chr15:100274128-100274178	A549	lung:	n/a
32	chr15:100274128-100274178	AG10803	skin:	n/a
33	chr15:100274128-100274178	NT2-D1	testis:	n/a
34	chr15:100274128-100274178	BE2_C	brain:	n/a
35	chr15:100274128-100274178	AG09309	skin:	n/a
36	chr15:100274128-100274178	HPAEpiC	pulmonary alveolar:	n/a
37	chr15:100274128-100274178	LNCaP	prostate:	n/a
38	chr15:100274128-100274178	HepG2	liver:	n/a
39	chr15:100274128-100274178	AG04450	lung:	fetal
40	chr15:100274128-100274178	GM12892	blood:	n/a
41	chr15:100274128-100274178	IMR90	lung:	fetal
42	chr15:100274128-100274178	PANC-1	pancreas:	n/a
43	chr15:100274128-100274178	Hela-S3	cervix:	n/a
44	chr15:100274128-100274178	GM12891	blood:	n/a
45	chr15:100274128-100274178	BJ	skin:	n/a
46	chr15:100274128-100274178	ECC-1	luminal epithelium:	n/a
47	chr15:100274128-100274178	HIPEpiC	eye:	n/a
48	chr15:100274128-100274178	HRPEpiC	eye:	n/a
49	chr15:100274128-100274178	Hepatocyte	liver:	n/a
50	chr15:100274128-100274178	GM19239	blood:	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:
5	chr15:99788657..99793033-chr15:100273651..100276844,5	MCF-7	breast:

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

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11631604	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12907407	0.86[EUR][1000 genomes]
rs1808723	0.84[ASN][1000 genomes]
rs2123927	0.84[ASN][1000 genomes]
rs2603221	0.84[ASN][1000 genomes]
rs35747287	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6598265	0.85[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8030331	LYSMD4	cis	Thyroid	GTEx
rs8030331	LYSMD4	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100271600-100274200	Active TSS	H9 Cell Line	embryonic stem cell
2	chr15:100271800-100274200	Active TSS	Rectal Smooth Muscle	rectum
3	chr15:100272000-100274200	Active TSS	NHLF	lung
4	chr15:100272200-100274200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:100272200-100274200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:100272200-100274200	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr15:100272400-100274200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:100272400-100274200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:100272400-100274200	Active TSS	Aorta	Aorta
10	chr15:100272400-100274200	Active TSS	Esophagus	oesophagus
11	chr15:100272400-100274200	Active TSS	Fetal Kidney	kidney
12	chr15:100272400-100274200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr15:100272400-100274200	Active TSS	Ovary	ovary
14	chr15:100272400-100274200	Active TSS	NHDF-Ad	bronchial
15	chr15:100272400-100274400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:100272600-100274200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:100272600-100274200	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr15:100272600-100274400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:100272800-100274200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:100272800-100274200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:100272800-100274200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:100272800-100274200	Active TSS	Brain Germinal Matrix	brain
23	chr15:100272800-100274200	Active TSS	Fetal Lung	lung
24	chr15:100272800-100274200	Active TSS	Small Intestine	intestine
25	chr15:100273000-100274200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:100273000-100274200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:100273000-100274200	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr15:100273000-100274200	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr15:100273000-100274200	Active TSS	Brain Anterior Caudate	brain
30	chr15:100273000-100274200	Active TSS	Brain Substantia Nigra	brain
31	chr15:100273000-100274200	Active TSS	Psoas Muscle	Psoas
32	chr15:100273000-100274200	Active TSS	HSMM	muscle
33	chr15:100273000-100274400	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr15:100273000-100274400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:100273000-100274400	Active TSS	HepG2	liver
36	chr15:100273200-100274200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:100273200-100274200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:100273200-100274200	Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr15:100273200-100274200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:100273200-100274200	Active TSS	Thymus	Thymus
41	chr15:100273200-100274200	Active TSS	NH-A	brain
42	chr15:100273200-100274400	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr15:100273200-100274400	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr15:100273200-100274400	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr15:100273200-100274400	Active TSS	Adipose Nuclei	Adipose
46	chr15:100273200-100274400	Active TSS	Stomach Smooth Muscle	stomach
47	chr15:100273400-100274200	Active TSS	Fetal Brain Female	brain
48	chr15:100273400-100274400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:100273400-100274400	Active TSS	Colonic Mucosa	Colon
50	chr15:100273800-100274200	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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