Variant report

Variant	rs213238
Chromosome Location	chr6:28321993-28321994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:79)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:79 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr6:28321863-28322095	K562	blood:	n/a	n/a
2	ATF1	chr6:28321765-28322269	K562	blood:	n/a	n/a
3	NFE2	chr6:28321820-28322300	K562	blood:	n/a	chr6:28322098-28322113
4	POLR2A	chr6:28321625-28325043	SK-N-MC	brain:	n/a	n/a
5	NFIC	chr6:28321604-28322404	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr6:28321642-28322023	ECC-1	luminal epithelium:	n/a	n/a
7	FOS	chr6:28321805-28322541	MCF10A-Er-Src	breast:	n/a	chr6:28322103-28322114
8	FOSL2	chr6:28321911-28322248	HepG2	liver:	n/a	n/a
9	BACH1	chr6:28321757-28322414	K562	blood:	n/a	n/a
10	MYC	chr6:28321696-28322357	MCF10A-Er-Src	breast:	n/a	n/a
11	TCF12	chr6:28321518-28322513	ECC-1	luminal epithelium:	n/a	n/a
12	FOS	chr6:28321934-28322391	HUVEC	blood vessel:	n/a	chr6:28322103-28322114
13	STAT3	chr6:28321914-28322464	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr6:28321563-28322164	ECC-1	luminal epithelium:	n/a	n/a
15	MAX	chr6:28321677-28322356	K562	blood:	n/a	n/a
16	POLR2A	chr6:28321455-28322146	K562	blood:	n/a	n/a
17	POLR2A	chr6:28321753-28322319	HCT-116	colon:	n/a	n/a
18	POLR2A	chr6:28321547-28322701	K562	blood:	n/a	n/a
19	MAX	chr6:28321680-28322394	ECC-1	luminal epithelium:	n/a	n/a
20	TBL1XR1	chr6:28321775-28322253	K562	blood:	n/a	n/a
21	CREB1	chr6:28321779-28322185	ECC-1	luminal epithelium:	n/a	n/a
22	FOS	chr6:28321834-28322558	MCF10A-Er-Src	breast:	n/a	chr6:28322103-28322114
23	POLR2A	chr6:28321594-28322463	PANC-1	pancreas:	n/a	n/a
24	EP300	chr6:28321700-28322242	K562	blood:	n/a	n/a
25	NFIC	chr6:28321557-28322450	ECC-1	luminal epithelium:	n/a	n/a
26	HCFC1	chr6:28321920-28322188	K562	blood:	n/a	n/a
27	MAFK	chr6:28321930-28322208	HepG2	liver:	n/a	n/a
28	NRF1	chr6:28321927-28322272	K562	blood:	n/a	chr6:28322083-28322094
29	MAFF	chr6:28321771-28322327	K562	blood:	n/a	n/a
30	FOS	chr6:28321715-28322456	MCF10A-Er-Src	breast:	n/a	chr6:28322103-28322114
31	MAX	chr6:28321767-28322229	K562	blood:	n/a	n/a
32	POLR2A	chr6:28321602-28322225	K562	blood:	n/a	n/a
33	ARID3A	chr6:28321731-28322157	K562	blood:	n/a	n/a
34	MAFF	chr6:28321912-28322126	HepG2	liver:	n/a	n/a
35	POLR2A	chr6:28321607-28322344	HUVEC	blood vessel:	n/a	n/a
36	TCF7L2	chr6:28321919-28322131	PANC-1	pancreas:	n/a	n/a
37	TEAD4	chr6:28321614-28322365	ECC-1	luminal epithelium:	n/a	n/a
38	CBX3	chr6:28321600-28322480	K562	blood:	n/a	n/a
39	POLR2A	chr6:28321678-28325465	K562	blood:	n/a	n/a
40	POLR2A	chr6:28321707-28322304	HUVEC	blood vessel:	n/a	n/a
41	TAL1	chr6:28321857-28322123	K562	blood:	n/a	n/a
42	CEBPB	chr6:28321903-28322159	K562	blood:	n/a	n/a
43	FOXA1	chr6:28321871-28322158	T-47D	breast:	n/a	n/a
44	FOS	chr6:28321944-28322508	MCF10A-Er-Src	breast:	n/a	chr6:28322103-28322114
45	POLR2A	chr6:28321505-28322309	K562	blood:	n/a	n/a
46	MAFK	chr6:28321782-28322309	K562	blood:	n/a	n/a
47	MAFK	chr6:28321882-28322139	HepG2	liver:	n/a	n/a
48	UBTF	chr6:28321641-28322047	K562	blood:	n/a	n/a
49	TEAD4	chr6:28321605-28322466	K562	blood:	n/a	n/a
50	YY1	chr6:28321687-28322349	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 49 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1005125	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs1052215	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[EUR][1000 genomes]
rs10946954	0.81[EUR][1000 genomes]
rs1124132	0.87[EUR][1000 genomes]
rs1150668	0.89[CEU][hapmap]
rs1150705	0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1150707	0.92[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs1150709	0.92[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1150711	0.86[JPT][hapmap]
rs1150716	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1150718	0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1150721	0.80[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1150724	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1150726	0.86[JPT][hapmap]
rs12214383	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs1225618	0.96[CEU][hapmap]
rs1233660	0.83[ASN][1000 genomes]
rs1233713	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13408	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs1531681	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs1736891	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs1736895	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs1778484	0.85[JPT][hapmap]
rs1997660	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2023493	0.87[EUR][1000 genomes]
rs213236	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs213237	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs213240	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2142730	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2247002	0.83[EUR][1000 genomes]
rs2394049	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs2531825	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2531831	0.83[EUR][1000 genomes]
rs2531832	0.87[EUR][1000 genomes]
rs2859348	0.82[CEU][hapmap];0.80[CHB][hapmap]
rs2859365	0.83[EUR][1000 genomes]
rs4455662	0.83[EUR][1000 genomes]
rs4713158	0.83[ASN][1000 genomes]
rs707907	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7206	0.92[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs728122	0.83[EUR][1000 genomes]
rs853683	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs853684	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853690	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs853693	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9301	0.87[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9368565	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9468333	1.00[JPT][hapmap];0.83[ASN][1000 genomes]

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

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs213238	ZSCAN31	cis	Muscle Skeletal	GTEx
rs213238	AL022393.7	cis	Heart Left Ventricle	GTEx
rs213238	AL022393.7	cis	Artery Tibial	GTEx
rs213238	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs213238	ZSCAN23	cis	Muscle Skeletal	GTEx
rs213238	ZSCAN31	cis	Thyroid	GTEx
rs213238	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs213238	ZNF323	cis	Frontal Cortex	GTEx
rs213238	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs213238	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs213238	ZSCAN31	cis	lung	GTEx
rs213238	ZSCAN23	cis	Artery Tibial	GTEx
rs213238	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs213238	AL022393.7	cis	Muscle Skeletal	GTEx
rs213238	AL022393.7	cis	lung	GTEx
rs213238	RP5-874C20.3	cis	Thyroid	GTEx
rs213238	AL022393.7	cis	Esophagus Muscularis	GTEx
rs213238	AL022393.7	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28317200-28322000	Active TSS	Rectal Smooth Muscle	rectum
2	chr6:28317200-28322200	Active TSS	Stomach Smooth Muscle	stomach
3	chr6:28318200-28322800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:28318400-28322200	Weak transcription	Placenta	Placenta
5	chr6:28318400-28323000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:28318400-28323600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:28318400-28332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:28318600-28322800	Weak transcription	NHDF-Ad	bronchial
10	chr6:28318600-28323000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr6:28318800-28322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:28318800-28322800	Weak transcription	Fetal Kidney	kidney
13	chr6:28319000-28323000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr6:28319000-28323200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr6:28319000-28323200	Weak transcription	Small Intestine	intestine
16	chr6:28319200-28322000	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr6:28319200-28322200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:28319200-28322200	Weak transcription	Lung	lung
19	chr6:28319200-28322200	Weak transcription	A549	lung
20	chr6:28319200-28322200	Weak transcription	HMEC	breast
21	chr6:28319200-28322400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:28319200-28322800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:28319200-28322800	Weak transcription	Right Ventricle	heart
24	chr6:28319200-28323000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:28319200-28323000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:28319200-28323000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:28319200-28323000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:28319200-28323000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:28319200-28323000	Weak transcription	Fetal Intestine Large	intestine
30	chr6:28319200-28323200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr6:28319200-28323200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr6:28319200-28323200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:28319200-28323200	Weak transcription	Fetal Intestine Small	intestine
34	chr6:28319200-28323400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:28319200-28323400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr6:28319200-28323600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr6:28319200-28323600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:28319200-28323600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:28319400-28322200	Weak transcription	Right Atrium	heart
40	chr6:28319400-28322200	Weak transcription	NH-A	brain
41	chr6:28319400-28322800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:28319400-28322800	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:28319400-28323000	Weak transcription	Brain Germinal Matrix	brain
44	chr6:28319400-28323000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr6:28319400-28323200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:28319400-28323400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr6:28319400-28323400	Weak transcription	Primary B cells from cord blood	blood
48	chr6:28319400-28323600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr6:28319600-28322800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:28319600-28322800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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