Variant report

Variant	rs213236
Chromosome Location	chr6:28324397-28324398
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28323493-28324505	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr6:28321625-28325043	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr6:28324289-28324548	HepG2	liver:	n/a	n/a
4	CTCF	chr6:28323069-28324565	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr6:28323359-28324405	HCT-116	colon:	n/a	n/a
6	CTCF	chr6:28324357-28324429	GM12892	blood:	n/a	n/a
7	CTCF	chr6:28323402-28324403	MCF-7	breast:	n/a	n/a
8	POLR2A	chr6:28323281-28324409	HUVEC	blood vessel:	n/a	n/a
9	ZBTB7A	chr6:28324128-28324429	K562	blood:	n/a	n/a
10	PML	chr6:28323587-28324401	GM12878	blood:	n/a	n/a
11	RAD21	chr6:28323308-28324556	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr6:28323469-28325125	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr6:28323226-28324407	K562	blood:	n/a	n/a
14	RAD21	chr6:28323366-28324438	HCT-116	colon:	n/a	n/a
15	POLR2A	chr6:28321678-28325465	K562	blood:	n/a	n/a
16	CTCF	chr6:28323276-28324446	A549	lung:	n/a	n/a
17	CTCF	chr6:28324340-28324490	GM12866	blood:	n/a	n/a
18	MAFK	chr6:28323910-28324414	H1-hESC	embryonic stem cell:	n/a	n/a
19	MTA3	chr6:28323390-28324466	GM12878	blood:	n/a	n/a
20	CTCF	chr6:28324380-28324530	GM12869	blood:	n/a	n/a
21	CTCF	chr6:28324328-28324399	GM19238	blood:	n/a	n/a
22	CTCF	chr6:28324372-28324460	GM19239	blood:	n/a	n/a
23	POLR2A	chr6:28323570-28324471	K562	blood:	n/a	n/a
24	CTCF	chr6:28324340-28324490	HEK293	kidney:	n/a	n/a
25	CBX3	chr6:28323339-28325251	K562	blood:	n/a	n/a
26	RAD21	chr6:28323318-28324507	HCT-116	colon:	n/a	n/a
27	SMC3	chr6:28323189-28324512	SK-N-SH	brain:	n/a	n/a
28	SP1	chr6:28323817-28324426	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr6:28324365-28324438	Fibrobl	skin:	n/a	n/a
30	CTCF	chr6:28324347-28324469	GM10266	blood:	n/a	n/a
31	POLR2A	chr6:28323397-28324495	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr6:28324340-28324490	GM12867	blood:	n/a	n/a
33	CTCF	chr6:28324349-28324475	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:28303323..28305430-chr6:28323198..28325730,3	MCF-7	breast:
2	chr6:28247781..28251138-chr6:28322226..28325499,4	K562	blood:
3	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
4	chr6:27780093..27783062-chr6:28322537..28324933,2	K562	blood:
5	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
6	chr6:27856204..27858764-chr6:28323949..28325832,2	K562	blood:
7	chr6:28219780..28221874-chr6:28323231..28325438,2	K562	blood:
8	chr6:27857264..27863272-chr6:28318615..28325449,9	K562	blood:
9	chr6:28109157..28111504-chr6:28323298..28325916,3	K562	blood:

No data

Variant related genes	Relation type
ZSCAN31	TF binding region
ENSG00000235109	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000182611	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000233224	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1005125	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1052215	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10946954	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1124132	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1150668	0.88[CEU][hapmap]
rs1150705	0.82[EUR][1000 genomes]
rs1150707	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1150709	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1150716	0.85[EUR][1000 genomes]
rs1150718	0.80[CHB][hapmap]
rs1150721	0.80[CHB][hapmap]
rs12214383	0.80[CEU][hapmap]
rs1225618	0.96[CEU][hapmap]
rs1233713	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs13408	0.80[CEU][hapmap]
rs1361387	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1531681	0.80[CEU][hapmap]
rs1736891	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1736895	0.80[CEU][hapmap]
rs2023493	0.94[EUR][1000 genomes]
rs213228	0.83[YRI][hapmap]
rs213232	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs213237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs213238	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs213240	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2142730	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2247002	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2394049	0.80[CHB][hapmap]
rs2531803	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.83[ASN][1000 genomes]
rs2531825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2531831	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2531832	0.94[EUR][1000 genomes]
rs2859348	0.89[CEU][hapmap];0.80[CHB][hapmap]
rs2859365	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4455662	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6938371	0.83[YRI][hapmap]
rs7206	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs728122	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853684	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs916403	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9301	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[EUR][1000 genomes]
rs9368565	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9468372	0.82[AMR][1000 genomes];0.87[EUR][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:22)

SNP	Gene	Cis/trans	Tissue	Source
rs213236	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs213236	ZSCAN31	cis	lung	GTEx
rs213236	ZSCAN23	cis	Stomach	GTEx
rs213236	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs213236	ZSCAN23	cis	Artery Tibial	GTEx
rs213236	ZSCAN23	cis	Muscle Skeletal	GTEx
rs213236	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs213236	TRIM27	cis	Skin Sun Exposed Lower leg	GTEx
rs213236	AL022393.7	cis	Nerve Tibial	GTEx
rs213236	ZSCAN31	cis	Thyroid	GTEx
rs213236	AL022393.7	cis	Artery Tibial	GTEx
rs213236	RP5-874C20.3	cis	Thyroid	GTEx
rs213236	ZSCAN31	cis	Muscle Skeletal	GTEx
rs213236	ZSCAN23	cis	lung	GTEx
rs213236	AL022393.7	cis	Heart Left Ventricle	GTEx
rs213236	AL022393.7	cis	Esophagus Muscularis	GTEx
rs213236	AL022393.7	cis	Artery Aorta	GTEx
rs213236	ZNF323	cis	Frontal Cortex	GTEx
rs213236	AL022393.7	cis	lung	GTEx
rs213236	AL022393.7	cis	Muscle Skeletal	GTEx
rs213236	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs213236	ZSCAN31	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28318400-28332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:28322200-28324600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr6:28322800-28324400	Flanking Active TSS	Liver	Liver
5	chr6:28323000-28324400	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr6:28323000-28324400	Flanking Active TSS	Dnd41	blood
7	chr6:28323000-28324400	Flanking Active TSS	K562	blood
8	chr6:28323000-28324800	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr6:28323000-28325000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:28323200-28324400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:28323200-28324400	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr6:28323200-28324600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:28323200-28324600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:28323200-28325000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr6:28323400-28324400	Flanking Active TSS	Fetal Brain Female	brain
16	chr6:28323400-28324400	Flanking Active TSS	Fetal Muscle Trunk	muscle
17	chr6:28323400-28324400	Flanking Active TSS	NHEK	skin
18	chr6:28323600-28324400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr6:28323600-28324400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr6:28323600-28324800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:28324000-28324400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr6:28324000-28324400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:28324000-28324400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr6:28324000-28324400	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr6:28324000-28324400	Enhancers	Spleen	Spleen
26	chr6:28324000-28324600	Enhancers	H1 Cell Line	embryonic stem cell
27	chr6:28324000-28324600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:28324000-28324600	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr6:28324000-28324600	Enhancers	Fetal Heart	heart
30	chr6:28324000-28324600	Enhancers	Left Ventricle	heart
31	chr6:28324000-28324600	Enhancers	Placenta Amnion	Placenta Amnion
32	chr6:28324000-28324600	Flanking Active TSS	HepG2	liver
33	chr6:28324000-28324800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:28324000-28324800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr6:28324000-28324800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:28324000-28324800	Enhancers	Lung	lung
37	chr6:28324000-28324800	Flanking Active TSS	Hela-S3	cervix
38	chr6:28324000-28325200	Enhancers	Gastric	stomach
39	chr6:28324000-28325600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:28324200-28324400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:28324200-28324400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:28324200-28324400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:28324200-28324400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:28324200-28324400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr6:28324200-28324400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:28324200-28324400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr6:28324200-28324400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:28324200-28324400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:28324200-28324400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:28324200-28324400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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