Variant report

Variant	rs213237
Chromosome Location	chr6:28323938-28323939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:193)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:193 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr6:28323731-28324314	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:28323450-28324302	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr6:28323849-28324262	A549	lung:	n/a	n/a
4	NFYA	chr6:28323696-28324054	Hela-S3	cervix:	n/a	n/a
5	FOXA1	chr6:28323928-28324162	T-47D	breast:	n/a	n/a
6	CTCF	chr6:28323839-28324327	HepG2	liver:	n/a	n/a
7	RFX5	chr6:28323510-28324224	Hela-S3	cervix:	n/a	n/a
8	YY1	chr6:28323618-28324231	SK-N-SH_RA	brain:	n/a	n/a
9	RAD21	chr6:28323461-28324308	SK-N-SH_RA	brain:	n/a	n/a
10	EP300	chr6:28323722-28324146	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:28323887-28324138	MCF-7	breast:	n/a	n/a
12	MAX	chr6:28323523-28324190	Hela-S3	cervix:	n/a	n/a
13	RAD21	chr6:28323516-28324285	GM12878	blood:	n/a	n/a
14	BHLHE40	chr6:28323602-28324246	GM12878	blood:	n/a	n/a
15	STAT5A	chr6:28323750-28324228	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:28323493-28324505	ECC-1	luminal epithelium:	n/a	n/a
17	MYC	chr6:28323552-28324186	K562	blood:	n/a	n/a
18	TEAD4	chr6:28323268-28324267	K562	blood:	n/a	n/a
19	POLR2A	chr6:28321625-28325043	SK-N-MC	brain:	n/a	n/a
20	SIN3A	chr6:28323571-28324257	H1-hESC	embryonic stem cell:	n/a	n/a
21	ZNF143	chr6:28323534-28324330	GM12878	blood:	n/a	n/a
22	CTCF	chr6:28323069-28324565	SK-N-SH	brain:	n/a	n/a
23	RAD21	chr6:28323373-28324252	MCF-7	breast:	n/a	n/a
24	CTCF	chr6:28323359-28324405	HCT-116	colon:	n/a	n/a
25	CTCF	chr6:28323908-28324216	HepG2	liver:	n/a	n/a
26	CEBPB	chr6:28323425-28324150	A549	lung:	n/a	n/a
27	NFIC	chr6:28323644-28324250	HepG2	liver:	n/a	n/a
28	TAF1	chr6:28323906-28324198	Hela-S3	cervix:	n/a	n/a
29	REST	chr6:28323740-28324177	A549	lung:	n/a	n/a
30	POLR2A	chr6:28323666-28324079	MCF10A-Er-Src	breast:	n/a	n/a
31	TCF12	chr6:28323473-28324224	A549	lung:	n/a	n/a
32	EBF1	chr6:28323677-28324260	GM12878	blood:	n/a	n/a
33	UBTF	chr6:28323505-28324136	K562	blood:	n/a	n/a
34	ATF2	chr6:28323775-28324219	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:28323253-28324192	K562	blood:	n/a	n/a
36	SIN3AK20	chr6:28323427-28324012	SK-N-SH	brain:	n/a	n/a
37	SMC3	chr6:28323361-28324274	Hela-S3	cervix:	n/a	n/a
38	RAD21	chr6:28323483-28324279	Hela-S3	cervix:	n/a	n/a
39	GTF2F1	chr6:28323543-28324202	Hela-S3	cervix:	n/a	n/a
40	RCOR1	chr6:28323473-28324245	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr6:28323402-28324403	MCF-7	breast:	n/a	n/a
42	STAT3	chr6:28323835-28324195	MCF10A-Er-Src	breast:	n/a	n/a
43	RCOR1	chr6:28323558-28324179	GM12878	blood:	n/a	n/a
44	MAX	chr6:28323477-28324263	K562	blood:	n/a	n/a
45	POLR2A	chr6:28323281-28324409	HUVEC	blood vessel:	n/a	n/a
46	HEY1	chr6:28323622-28324142	K562	blood:	n/a	n/a
47	POLR2A	chr6:28323530-28324142	HepG2	liver:	n/a	n/a
48	SIN3AK20	chr6:28323511-28324317	PANC-1	pancreas:	n/a	n/a
49	POU2F2	chr6:28323568-28324314	GM12878	blood:	n/a	n/a
50	TEAD4	chr6:28323857-28324375	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:11 , 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	chr6:28219780..28221874-chr6:28323231..28325438,2	K562	blood:
7	chr6:27857264..27863272-chr6:28318615..28325449,9	K562	blood:
8	chr6:28102102..28105139-chr6:28322040..28324310,3	K562	blood:
9	chr6:28314766..28319001-chr6:28320941..28324187,4	MCF-7	breast:
10	chr6:28109157..28111504-chr6:28323298..28325916,3	K562	blood:
11	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:

No data

Variant related genes	Relation type
ZSCAN31	TF binding region
ENSG00000196331	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000182611	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000198315	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 33 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1005125	0.95[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1052215	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10946954	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1124132	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1150668	0.88[CEU][hapmap]
rs1150705	0.82[EUR][1000 genomes]
rs1150707	0.92[CEU][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes]
rs1150709	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1150716	0.85[EUR][1000 genomes]
rs1150724	0.81[CHD][hapmap]
rs12214383	0.81[CEU][hapmap]
rs1225618	0.96[CEU][hapmap];0.84[MEX][hapmap]
rs1233713	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs13408	0.81[CEU][hapmap]
rs1531681	0.81[CEU][hapmap]
rs1558205	0.81[TSI][hapmap]
rs1736891	0.92[CEU][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs1736895	0.81[CEU][hapmap]
rs2023493	0.94[EUR][1000 genomes]
rs213228	0.83[YRI][hapmap]
rs213232	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs213236	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];0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2142730	0.92[CEU][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes]
rs2247002	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2531803	0.81[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.95[YRI][hapmap]
rs2531825	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2531831	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2531832	0.94[EUR][1000 genomes]
rs2859348	0.88[CEU][hapmap]
rs2859365	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4455662	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6938371	0.81[YRI][hapmap]
rs7206	0.92[CEU][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes]
rs728122	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs853684	0.92[CEU][hapmap];0.84[MEX][hapmap];0.86[EUR][1000 genomes]
rs916403	0.88[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.95[YRI][hapmap]
rs9301	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[EUR][1000 genomes]
rs9368565	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9468372	0.81[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:33)

SNP	Gene	Cis/trans	Tissue	Source
rs213237	ZSCAN31	cis	Muscle Skeletal	GTEx
rs213237	ZKSCAN3	cis	cerebellum	SCAN
rs213237	ZNF187	cis	cerebellum	SCAN
rs213237	ZSCAN23	cis	cerebellum	SCAN
rs213237	TRIM27	cis	Skin Sun Exposed Lower leg	GTEx
rs213237	ZNF192	cis	cerebellum	SCAN
rs213237	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs213237	ZSCAN23	cis	lung	GTEx
rs213237	ZNF323	cis	Frontal Cortex	GTEx
rs213237	RP5-874C20.3	cis	Thyroid	GTEx
rs213237	AL022393.7	cis	Artery Aorta	GTEx
rs213237	AL022393.7	cis	Artery Tibial	GTEx
rs213237	ZSCAN31	cis	Thyroid	GTEx
rs213237	ZSCAN23	cis	Artery Tibial	GTEx
rs213237	ZNF323	cis	cerebellum	SCAN
rs213237	ZSCAN23	cis	Stomach	GTEx
rs213237	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs213237	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs213237	ZSCAN31	cis	lung	GTEx
rs213237	AL022393.7	cis	Heart Left Ventricle	GTEx
rs213237	AL022393.7	cis	Esophagus Muscularis	GTEx
rs213237	AL022393.7	cis	lung	GTEx
rs213237	ZSCAN23	cis	Muscle Skeletal	GTEx
rs213237	AL022393.7	cis	Nerve Tibial	GTEx
rs213237	ZSCAN23	cis	parietal	SCAN
rs213237	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs213237	ZKSCAN3	cis	parietal	SCAN
rs213237	NKAPL	cis	parietal	SCAN
rs213237	AL022393.7	cis	Muscle Skeletal	GTEx
rs213237	ZSCAN23	cis	lymphoblastoid	seeQTL
rs213237	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs213237	HIST1H2BL	cis	cerebellum	SCAN
rs213237	ZNF323	cis	parietal	SCAN

Chromatin state (count:127 , 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	chr6:28323000-28324200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:28323000-28324200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:28323000-28324400	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr6:28323000-28324400	Flanking Active TSS	Dnd41	blood
9	chr6:28323000-28324400	Flanking Active TSS	K562	blood
10	chr6:28323000-28324800	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr6:28323000-28325000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:28323200-28324400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:28323200-28324400	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr6:28323200-28324600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:28323200-28324600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:28323200-28325000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr6:28323400-28324000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr6:28323400-28324000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr6:28323400-28324000	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr6:28323400-28324000	Active TSS	Left Ventricle	heart
21	chr6:28323400-28324200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:28323400-28324200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:28323400-28324200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:28323400-28324200	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr6:28323400-28324200	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr6:28323400-28324200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr6:28323400-28324200	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr6:28323400-28324200	Active TSS	Brain Hippocampus Middle	brain
29	chr6:28323400-28324200	Active TSS	Colon Smooth Muscle	Colon
30	chr6:28323400-28324200	Flanking Active TSS	Fetal Brain Male	brain
31	chr6:28323400-28324200	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr6:28323400-28324200	Flanking Active TSS	Fetal Stomach	stomach
33	chr6:28323400-28324200	Active TSS	Ovary	ovary
34	chr6:28323400-28324200	Flanking Active TSS	GM12878-XiMat	blood
35	chr6:28323400-28324400	Flanking Active TSS	Fetal Brain Female	brain
36	chr6:28323400-28324400	Flanking Active TSS	Fetal Muscle Trunk	muscle
37	chr6:28323400-28324400	Flanking Active TSS	NHEK	skin
38	chr6:28323600-28324000	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr6:28323600-28324000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
40	chr6:28323600-28324000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:28323600-28324000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:28323600-28324000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:28323600-28324000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:28323600-28324000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr6:28323600-28324000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr6:28323600-28324000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr6:28323600-28324000	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:28323600-28324000	Active TSS	Primary monocytes fromperipheralblood	blood
49	chr6:28323600-28324000	Active TSS	Aorta	Aorta
50	chr6:28323600-28324000	Active TSS	Fetal Heart	heart

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