Variant report

Variant	rs6456814
Chromosome Location	chr6:28305812-28305813
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr6:28300330-28306374	K562	blood:	n/a	chr6:28300992-28301002 chr6:28304956-28304965 chr6:28304017-28304027
2	POLR2A	chr6:28302878-28306282	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:28305716-28305976	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:28303038-28306300	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:28302772-28306469	K562	blood:	n/a	n/a
6	POLR2A	chr6:28302783-28305842	K562	blood:	n/a	n/a
7	NR2F2	chr6:28302362-28305837	K562	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28305023..28307714-chr6:28355958..28358291,2	K562	blood:
2	chr6:28191649..28195458-chr6:28301378..28307708,9	K562	blood:
3	chr6:28099723..28110178-chr6:28301599..28306918,14	K562	blood:
4	chr6:28247415..28251168-chr6:28301808..28306623,8	K562	blood:
5	chr6:28302870..28305047-chr6:28305335..28307557,3	MCF-7	breast:
6	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
7	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
8	chr6:28233221..28238495-chr6:28301018..28307259,12	K562	blood:
9	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
10	chr6:28233528..28236356-chr6:28305759..28308573,2	K562	blood:
11	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:
12	chr6:28304462..28306809-chr6:28341388..28343447,2	K562	blood:
13	chr6:27857690..27865363-chr6:28300493..28306970,14	K562	blood:

No data

Variant related genes	Relation type
ZSCAN31	TF binding region
ENSG00000233224	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000238610	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000197153	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1062169	0.80[ASN][1000 genomes]
rs1119211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150713	0.80[ASN][1000 genomes]
rs1150714	0.80[ASN][1000 genomes]
rs1150717	0.80[ASN][1000 genomes]
rs1150720	0.80[ASN][1000 genomes]
rs11970439	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13210258	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17301128	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1778477	0.80[ASN][1000 genomes]
rs1778478	0.80[ASN][1000 genomes]
rs2281043	0.80[ASN][1000 genomes]
rs2799081	0.81[EUR][1000 genomes]
rs3800325	0.80[ASN][1000 genomes]
rs56053755	0.80[ASN][1000 genomes]
rs56131013	0.91[EUR][1000 genomes]
rs6456811	0.80[ASN][1000 genomes]
rs6456816	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6903652	0.91[EUR][1000 genomes]
rs6903823	0.90[EUR][1000 genomes]
rs6912584	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6921919	0.82[EUR][1000 genomes]
rs6922111	0.82[EUR][1000 genomes]
rs6923170	0.80[ASN][1000 genomes]
rs9468350	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6456814	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs6456814	ZSCAN23	cis	Artery Tibial	GTEx
rs6456814	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs6456814	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs6456814	RP5-874C20.3	cis	Thyroid	GTEx
rs6456814	ZSCAN23	cis	Muscle Skeletal	GTEx
rs6456814	AL022393.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28304400-28317400	Weak transcription	Pancreas	Pancrea
2	chr6:28304800-28317200	Weak transcription	Aorta	Aorta
3	chr6:28305000-28306200	Enhancers	Primary hematopoietic stem cells	blood
4	chr6:28305000-28310000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:28305000-28317200	Weak transcription	Brain Anterior Caudate	brain
6	chr6:28305000-28317200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:28305200-28308000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr6:28305200-28308000	Weak transcription	Fetal Stomach	stomach
9	chr6:28305200-28311800	Weak transcription	Brain Angular Gyrus	brain
10	chr6:28305200-28313800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:28305200-28317000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:28305200-28317000	Weak transcription	NHEK	skin
13	chr6:28305200-28317200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:28305200-28317200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:28305200-28317200	Weak transcription	HSMMtube	muscle
16	chr6:28305400-28306200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr6:28305400-28306800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:28305600-28306000	Weak transcription	Fetal Kidney	kidney
19	chr6:28305800-28306400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:28305800-28306400	Enhancers	K562	blood
21	chr6:28305800-28317200	Weak transcription	Stomach Smooth Muscle	stomach

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