Variant report

Variant	rs6903823
Chromosome Location	chr6:28322296-28322297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFE2	chr6:28321820-28322300	K562	blood:	n/a	chr6:28322098-28322113
2	POLR2A	chr6:28321625-28325043	SK-N-MC	brain:	n/a	n/a
3	NFIC	chr6:28321604-28322404	ECC-1	luminal epithelium:	n/a	n/a
4	FOS	chr6:28321805-28322541	MCF10A-Er-Src	breast:	n/a	chr6:28322103-28322114
5	BCL3	chr6:28322132-28322453	GM12878	blood:	n/a	n/a
6	BACH1	chr6:28321757-28322414	K562	blood:	n/a	n/a
7	MYC	chr6:28321696-28322357	MCF10A-Er-Src	breast:	n/a	n/a
8	TCF12	chr6:28321518-28322513	ECC-1	luminal epithelium:	n/a	n/a
9	FOS	chr6:28321934-28322391	HUVEC	blood vessel:	n/a	chr6:28322103-28322114
10	STAT3	chr6:28321914-28322464	MCF10A-Er-Src	breast:	n/a	n/a
11	MAX	chr6:28321677-28322356	K562	blood:	n/a	n/a
12	POLR2A	chr6:28321753-28322319	HCT-116	colon:	n/a	n/a
13	POLR2A	chr6:28321547-28322701	K562	blood:	n/a	n/a
14	MAX	chr6:28321680-28322394	ECC-1	luminal epithelium:	n/a	n/a
15	FOS	chr6:28321834-28322558	MCF10A-Er-Src	breast:	n/a	chr6:28322103-28322114
16	POLR2A	chr6:28321594-28322463	PANC-1	pancreas:	n/a	n/a
17	NFIC	chr6:28321557-28322450	ECC-1	luminal epithelium:	n/a	n/a
18	MAFF	chr6:28321771-28322327	K562	blood:	n/a	n/a
19	FOS	chr6:28321715-28322456	MCF10A-Er-Src	breast:	n/a	chr6:28322103-28322114
20	POLR2A	chr6:28321607-28322344	HUVEC	blood vessel:	n/a	n/a
21	TEAD4	chr6:28321614-28322365	ECC-1	luminal epithelium:	n/a	n/a
22	CBX3	chr6:28321600-28322480	K562	blood:	n/a	n/a
23	POLR2A	chr6:28321678-28325465	K562	blood:	n/a	n/a
24	POLR2A	chr6:28321707-28322304	HUVEC	blood vessel:	n/a	n/a
25	FOS	chr6:28321944-28322508	MCF10A-Er-Src	breast:	n/a	chr6:28322103-28322114
26	POLR2A	chr6:28321505-28322309	K562	blood:	n/a	n/a
27	MAFK	chr6:28321782-28322309	K562	blood:	n/a	n/a
28	TEAD4	chr6:28321605-28322466	K562	blood:	n/a	n/a
29	YY1	chr6:28321687-28322349	ECC-1	luminal epithelium:	n/a	n/a
30	SETDB1	chr6:28321902-28322388	U2OS	brain:	n/a	n/a
31	KAP1	chr6:28321766-28322354	HEK293	kidney:	n/a	n/a
32	POLR2A	chr6:28321585-28322476	HUVEC	blood vessel:	n/a	n/a
33	E2F4	chr6:28322054-28322452	MCF10A-Er-Src	breast:	n/a	n/a
34	RCOR1	chr6:28321758-28322309	K562	blood:	n/a	n/a
35	POLR2A	chr6:28321746-28322310	HCT-116	colon:	n/a	n/a
36	STAT3	chr6:28321850-28322455	MCF10A-Er-Src	breast:	n/a	n/a
37	TCF12	chr6:28321649-28322380	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr6:28321689-28322405	PANC-1	pancreas:	n/a	n/a
39	MYC	chr6:28321857-28322455	MCF10A-Er-Src	breast:	n/a	n/a
40	MAX	chr6:28321614-28322504	ECC-1	luminal epithelium:	n/a	n/a
41	IRF1	chr6:28321896-28322309	K562	blood:	n/a	n/a
42	TEAD4	chr6:28321641-28322420	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr6:28322237-28322456	MCF10A-Er-Src	breast:	n/a	n/a
44	NR2F2	chr6:28321148-28323272	K562	blood:	n/a	n/a
45	EP300	chr6:28321557-28322520	ECC-1	luminal epithelium:	n/a	n/a
46	YY1	chr6:28321650-28322415	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28247781..28251138-chr6:28322226..28325499,4	K562	blood:
2	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
3	chr6:27860028..27861689-chr6:28321850..28323929,2	K562	blood:
4	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
5	chr6:28108695..28111169-chr6:28321228..28323056,2	K562	blood:
6	chr6:27857264..27863272-chr6:28318615..28325449,9	K562	blood:
7	chr6:28102102..28105139-chr6:28322040..28324310,3	K562	blood:
8	chr6:28314766..28319001-chr6:28320941..28324187,4	MCF-7	breast:
9	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:

No data

Variant related genes	Relation type
ZSCAN31	TF binding region
ENSG00000197153	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000137185	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1119211	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs11756111	0.88[JPT][hapmap]
rs11758148	0.88[JPT][hapmap]
rs11758337	0.84[JPT][hapmap]
rs11970439	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13210258	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs1474589	0.88[JPT][hapmap]
rs16893937	0.88[JPT][hapmap]
rs16894116	0.83[CEU][hapmap]
rs16901847	0.83[CEU][hapmap]
rs17301128	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17312661	0.88[CEU][hapmap]
rs17776284	0.88[JPT][hapmap]
rs2185955	0.88[JPT][hapmap]
rs2235358	0.88[JPT][hapmap]
rs2235359	0.88[JPT][hapmap]
rs2299031	0.88[JPT][hapmap]
rs35875412	0.81[EUR][1000 genomes]
rs3800326	0.88[JPT][hapmap]
rs56131013	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456814	0.90[EUR][1000 genomes]
rs6456816	0.89[EUR][1000 genomes]
rs6903652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912584	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6921919	0.94[CEU][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6922111	0.94[CEU][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7766356	0.88[CEU][hapmap]
rs7769054	0.88[JPT][hapmap]
rs9468350	0.94[EUR][1000 genomes]
rs993619	0.88[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Pulmonary function	21946350	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6903823	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs6903823	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs6903823	ZSCAN23	cis	Muscle Skeletal	GTEx
rs6903823	ZSCAN23	cis	Artery Tibial	GTEx
rs6903823	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs6903823	AL022393.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28318200-28322800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:28318400-28323000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:28318400-28323600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:28318400-28332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:28318600-28322800	Weak transcription	NHDF-Ad	bronchial
7	chr6:28318600-28323000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr6:28318800-28322800	Weak transcription	Fetal Kidney	kidney
9	chr6:28319000-28323000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr6:28319000-28323200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr6:28319000-28323200	Weak transcription	Small Intestine	intestine
12	chr6:28319200-28322400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:28319200-28322800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:28319200-28322800	Weak transcription	Right Ventricle	heart
15	chr6:28319200-28323000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:28319200-28323000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:28319200-28323000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:28319200-28323000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:28319200-28323000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:28319200-28323000	Weak transcription	Fetal Intestine Large	intestine
21	chr6:28319200-28323200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr6:28319200-28323200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr6:28319200-28323200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:28319200-28323200	Weak transcription	Fetal Intestine Small	intestine
25	chr6:28319200-28323400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:28319200-28323400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr6:28319200-28323600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:28319200-28323600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:28319200-28323600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:28319400-28322800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:28319400-28322800	Weak transcription	Colon Smooth Muscle	Colon
32	chr6:28319400-28323000	Weak transcription	Brain Germinal Matrix	brain
33	chr6:28319400-28323000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr6:28319400-28323200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:28319400-28323400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:28319400-28323400	Weak transcription	Primary B cells from cord blood	blood
37	chr6:28319400-28323600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr6:28319600-28322800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:28319600-28322800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr6:28319600-28322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:28319600-28322800	Weak transcription	Fetal Lung	lung
42	chr6:28319600-28322800	Weak transcription	Hela-S3	cervix
43	chr6:28319600-28323000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr6:28319600-28323000	Weak transcription	Brain Substantia Nigra	brain
45	chr6:28319600-28323000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr6:28319600-28323000	Weak transcription	Fetal Brain Male	brain
47	chr6:28319600-28323000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:28319600-28323200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:28319600-28323200	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr6:28319600-28323400	Weak transcription	Fetal Brain Female	brain

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