Variant report

Variant	rs13198809
Chromosome Location	chr6:28323702-28323703
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:225)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:225 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:28323516-28323794	NHEK	skin:	n/a	n/a
2	POLR2A	chr6:28323450-28324302	Hela-S3	cervix:	n/a	n/a
3	NFYA	chr6:28323696-28324054	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr6:28323600-28323750	HUVEC	blood vessel:	n/a	n/a
5	CTCF	chr6:28323620-28323770	AoAF	blood vessel:	n/a	n/a
6	CTCF	chr6:28323560-28323710	SAEC	small airway:	n/a	n/a
7	CTCF	chr6:28323560-28323710	HMF	breast:	n/a	n/a
8	CTCF	chr6:28323580-28323730	AG10803	skin:	n/a	n/a
9	CTCF	chr6:28323536-28323784	ProgFib	skin:	n/a	n/a
10	RFX5	chr6:28323510-28324224	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr6:28323519-28323782	MCF-7	breast:	n/a	n/a
12	YY1	chr6:28323618-28324231	SK-N-SH_RA	brain:	n/a	n/a
13	CTCF	chr6:28323527-28323713	HepG2	liver:	n/a	n/a
14	RAD21	chr6:28323461-28324308	SK-N-SH_RA	brain:	n/a	n/a
15	MAX	chr6:28323523-28324190	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr6:28323600-28323750	A549	lung:	n/a	n/a
17	RAD21	chr6:28323516-28324285	GM12878	blood:	n/a	n/a
18	BHLHE40	chr6:28323602-28324246	GM12878	blood:	n/a	n/a
19	CTCF	chr6:28323620-28323770	AG04450	lung:	n/a	n/a
20	POLR2A	chr6:28323493-28324505	ECC-1	luminal epithelium:	n/a	n/a
21	MYC	chr6:28323552-28324186	K562	blood:	n/a	n/a
22	TEAD4	chr6:28323268-28324267	K562	blood:	n/a	n/a
23	POLR2A	chr6:28321625-28325043	SK-N-MC	brain:	n/a	n/a
24	SIN3A	chr6:28323571-28324257	H1-hESC	embryonic stem cell:	n/a	n/a
25	ZNF143	chr6:28323534-28324330	GM12878	blood:	n/a	n/a
26	CTCF	chr6:28323069-28324565	SK-N-SH	brain:	n/a	n/a
27	RAD21	chr6:28323373-28324252	MCF-7	breast:	n/a	n/a
28	CTCF	chr6:28323510-28323805	MCF-7	breast:	n/a	n/a
29	CTCF	chr6:28323359-28324405	HCT-116	colon:	n/a	n/a
30	CEBPB	chr6:28323425-28324150	A549	lung:	n/a	n/a
31	NFIC	chr6:28323644-28324250	HepG2	liver:	n/a	n/a
32	POLR2A	chr6:28323666-28324079	MCF10A-Er-Src	breast:	n/a	n/a
33	TCF12	chr6:28323473-28324224	A549	lung:	n/a	n/a
34	EBF1	chr6:28323677-28324260	GM12878	blood:	n/a	n/a
35	UBTF	chr6:28323505-28324136	K562	blood:	n/a	n/a
36	POLR2A	chr6:28323253-28324192	K562	blood:	n/a	n/a
37	SIN3AK20	chr6:28323427-28324012	SK-N-SH	brain:	n/a	n/a
38	SMC3	chr6:28323361-28324274	Hela-S3	cervix:	n/a	n/a
39	RAD21	chr6:28323483-28324279	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr6:28323620-28323770	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr6:28323553-28323711	GM10266	blood:	n/a	n/a
42	CTCF	chr6:28323580-28323730	HFF-Myc	foreskin:	n/a	n/a
43	CTCF	chr6:28323529-28323740	LNCaP	prostate:	n/a	n/a
44	GTF2F1	chr6:28323543-28324202	Hela-S3	cervix:	n/a	n/a
45	RCOR1	chr6:28323473-28324245	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr6:28323402-28324403	MCF-7	breast:	n/a	n/a
47	RCOR1	chr6:28323558-28324179	GM12878	blood:	n/a	n/a
48	CTCF	chr6:28323521-28323758	GM12878	blood:	n/a	n/a
49	MAX	chr6:28323477-28324263	K562	blood:	n/a	n/a
50	POLR2A	chr6:28323281-28324409	HUVEC	blood vessel:	n/a	n/a

No data

(count:12 , 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	chr6:27860028..27861689-chr6:28321850..28323929,2	K562	blood:
6	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
7	chr6:28219780..28221874-chr6:28323231..28325438,2	K562	blood:
8	chr6:27857264..27863272-chr6:28318615..28325449,9	K562	blood:
9	chr6:28102102..28105139-chr6:28322040..28324310,3	K562	blood:
10	chr6:28314766..28319001-chr6:28320941..28324187,4	MCF-7	breast:
11	chr6:28109157..28111504-chr6:28323298..28325916,3	K562	blood:
12	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:

No data

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

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs13190888	0.88[EUR][1000 genomes]
rs13191038	0.93[EUR][1000 genomes]
rs13191786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13195291	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13197633	0.93[EUR][1000 genomes]
rs13201308	0.85[EUR][1000 genomes]
rs13201681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13204012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13205211	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13205911	0.85[EUR][1000 genomes]
rs13207345	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13208096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13211507	0.93[EUR][1000 genomes]
rs13213152	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13213986	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13214023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13217619	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13217984	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2232423	0.96[EUR][1000 genomes]
rs2232426	0.96[EUR][1000 genomes]
rs2232429	0.96[EUR][1000 genomes]
rs33932084	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34218844	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34243448	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34396849	0.93[EUR][1000 genomes]
rs34505829	0.85[EUR][1000 genomes]
rs34546986	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34661125	0.93[EUR][1000 genomes]
rs34676049	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34691223	0.93[EUR][1000 genomes]
rs34765154	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34832585	0.85[EUR][1000 genomes]
rs34871267	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34878803	0.93[EUR][1000 genomes]
rs34950484	0.93[EUR][1000 genomes]
rs35001169	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35016036	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35017208	1.00[EUR][1000 genomes]
rs35030260	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35072899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35098436	0.85[EUR][1000 genomes]
rs35345226	0.85[EUR][1000 genomes]
rs35353359	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35656932	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35744819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35749575	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35781323	0.85[EUR][1000 genomes]
rs35883476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36092177	0.96[EUR][1000 genomes]
rs55690788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56075693	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56189111	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66886492	0.85[EUR][1000 genomes]
rs67297533	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs67340775	0.94[EUR][1000 genomes]
rs67381177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67981811	0.96[EUR][1000 genomes]
rs67998226	0.93[EUR][1000 genomes]
rs71559072	0.85[EUR][1000 genomes]
rs72846780	0.85[EUR][1000 genomes]
rs72846794	0.85[EUR][1000 genomes]
rs72854513	1.00[AMR][1000 genomes];0.93[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13198809	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs13198809	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13198809	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13198809	AL022393.7	cis	Muscle Skeletal	GTEx

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	chr6:28322800-28323800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:28322800-28323800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr6:28322800-28324400	Flanking Active TSS	Liver	Liver
7	chr6:28323000-28323800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:28323000-28323800	Flanking Active TSS	HMEC	breast
9	chr6:28323000-28324200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:28323000-28324200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:28323000-28324400	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr6:28323000-28324400	Flanking Active TSS	Dnd41	blood
13	chr6:28323000-28324400	Flanking Active TSS	K562	blood
14	chr6:28323000-28324800	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr6:28323000-28325000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:28323200-28323800	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr6:28323200-28323800	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr6:28323200-28323800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr6:28323200-28323800	Flanking Active TSS	Rectal Smooth Muscle	rectum
20	chr6:28323200-28324400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:28323200-28324400	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr6:28323200-28324600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:28323200-28324600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:28323200-28325000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr6:28323400-28323800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr6:28323400-28323800	Flanking Active TSS	Fetal Lung	lung
27	chr6:28323400-28323800	Flanking Active TSS	Placenta	Placenta
28	chr6:28323400-28323800	Flanking Active TSS	Fetal Thymus	thymus
29	chr6:28323400-28323800	Flanking Active TSS	Pancreas	Pancrea
30	chr6:28323400-28323800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr6:28323400-28323800	Active TSS	HSMMtube	muscle
32	chr6:28323400-28323800	Flanking Active TSS	HUVEC	blood vessel
33	chr6:28323400-28324000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr6:28323400-28324000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr6:28323400-28324000	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr6:28323400-28324000	Active TSS	Left Ventricle	heart
37	chr6:28323400-28324200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:28323400-28324200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:28323400-28324200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:28323400-28324200	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr6:28323400-28324200	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr6:28323400-28324200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr6:28323400-28324200	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr6:28323400-28324200	Active TSS	Brain Hippocampus Middle	brain
45	chr6:28323400-28324200	Active TSS	Colon Smooth Muscle	Colon
46	chr6:28323400-28324200	Flanking Active TSS	Fetal Brain Male	brain
47	chr6:28323400-28324200	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr6:28323400-28324200	Flanking Active TSS	Fetal Stomach	stomach
49	chr6:28323400-28324200	Active TSS	Ovary	ovary
50	chr6:28323400-28324200	Flanking Active TSS	GM12878-XiMat	blood

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