Variant report

Variant	rs9393929
Chromosome Location	chr6:28696063-28696064
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr6:28696013-28696204	K562	blood:	n/a	n/a
2	IRF1	chr6:28694816-28696122	K562	blood:	n/a	chr6:28694954-28694968 chr6:28695568-28695579 chr6:28694950-28694964 chr6:28695259-28695273 chr6:28695566-28695580 chr6:28695567-28695578 chr6:28694952-28694972 chr6:28695565-28695579 chr6:28694992-28695004 chr6:28695567-28695581 chr6:28695565-28695585 chr6:28694954-28694964
3	ARID3A	chr6:28693225-28696326	K562	blood:	n/a	chr6:28693710-28693726
4	SREBP2	chr6:28695765-28697599	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28695857..28698165-chr6:28761272..28763967,2	K562	blood:
2	chr6:28695149..28697621-chr6:28743260..28745137,3	K562	blood:
3	chr6:28694596..28696864-chr6:28727942..28730829,2	K562	blood:
4	chr6:28694465..28699409-chr6:28701823..28706376,12	K562	blood:
5	chr6:28694415..28696951-chr6:28906885..28909854,2	K562	blood:
6	chr6:28695047..28697144-chr6:28756622..28759292,2	K562	blood:
7	chr6:28649222..28651616-chr6:28694274..28696265,2	MCF-7	breast:
8	chr6:28694600..28696603-chr6:28717973..28720482,2	K562	blood:
9	chr6:28666298..28671313-chr6:28695437..28699521,5	K562	blood:
10	chr6:28694799..28697435-chr6:28950609..28952532,2	K562	blood:
11	chr6:28695842..28698712-chr6:28863478..28865661,2	K562	blood:
12	chr6:28695559..28699343-chr6:28721391..28727067,6	K562	blood:
13	chr6:28693769..28696400-chr6:28804513..28806706,3	K562	blood:
14	chr6:27859745..27862203-chr6:28694070..28696885,3	K562	blood:
15	chr6:28695552..28697065-chr6:28863469..28865402,2	K562	blood:
16	chr6:28693500..28696718-chr6:28743195..28744760,3	K562	blood:
17	chr6:28695145..28698066-chr6:28723238..28727067,5	K562	blood:
18	chr6:28693622..28696352-chr6:28828631..28830226,2	K562	blood:
19	chr6:28695685..28697357-chr6:28761253..28763967,2	K562	blood:
20	chr6:28693863..28696096-chr6:28729329..28732311,2	K562	blood:

Variant related genes	Relation type
RPSAP2	TF binding region
ENSG00000233224	Chromatin interaction
ENSG00000221191	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000265764	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000213916	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1233579	0.88[EUR][1000 genomes]
rs1233580	0.88[EUR][1000 genomes]
rs1233581	0.88[EUR][1000 genomes]
rs1233583	0.88[EUR][1000 genomes]
rs1233593	0.88[EUR][1000 genomes]
rs1233594	0.88[EUR][1000 genomes]
rs1233599	0.84[EUR][1000 genomes]
rs1233600	0.84[EUR][1000 genomes]
rs1233604	0.84[EUR][1000 genomes]
rs1233618	0.84[EUR][1000 genomes]
rs1233620	0.84[EUR][1000 genomes]
rs1233623	0.84[EUR][1000 genomes]
rs1238262	0.88[EUR][1000 genomes]
rs1311911	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1311912	0.88[EUR][1000 genomes]
rs1311913	0.88[EUR][1000 genomes]
rs13194504	0.89[EUR][1000 genomes]
rs13217472	0.95[EUR][1000 genomes]
rs1742743	0.86[EUR][1000 genomes]
rs34724414	0.89[EUR][1000 genomes]
rs35044849	0.89[EUR][1000 genomes]
rs35243068	0.95[EUR][1000 genomes]
rs6456835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6908726	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7764642	0.82[EUR][1000 genomes]
rs9257133	0.88[EUR][1000 genomes]
rs9257136	0.88[EUR][1000 genomes]
rs9257137	0.88[EUR][1000 genomes]
rs9257140	0.88[EUR][1000 genomes]
rs9257167	0.84[EUR][1000 genomes]
rs9257183	0.84[EUR][1000 genomes]
rs9257184	0.84[EUR][1000 genomes]
rs9257187	0.84[EUR][1000 genomes]
rs9257188	0.84[EUR][1000 genomes]
rs9257189	0.84[EUR][1000 genomes]
rs9257192	0.84[EUR][1000 genomes]
rs9393926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[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	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9393929	BTN3A2	trans	lymphoblastoid	seeQTL
rs9393929	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9393929	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs9393929	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs9393929	ZFP57	cis	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28693600-28696200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:28693800-28696200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:28694200-28697800	Active TSS	K562	blood
4	chr6:28695400-28696200	Bivalent Enhancer	HepG2	liver
5	chr6:28695600-28696200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr6:28695600-28696200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:28695600-28696200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr6:28695600-28696200	Flanking Active TSS	A549	lung
9	chr6:28695600-28696200	Enhancers	GM12878-XiMat	blood
10	chr6:28695800-28696200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:28695800-28696200	Bivalent Enhancer	HUVEC	blood vessel
12	chr6:28695800-28696200	Enhancers	NHLF	lung
13	chr6:28695800-28696400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:28695800-28696400	Bivalent Enhancer	Dnd41	blood
15	chr6:28695800-28698000	Active TSS	NH-A	brain
16	chr6:28695800-28698200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:28695800-28698200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr6:28696000-28696200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:28696000-28696200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr6:28696000-28696400	Bivalent Enhancer	Fetal Lung	lung
21	chr6:28696000-28696400	Active TSS	Stomach Smooth Muscle	stomach
22	chr6:28696000-28696600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:28696000-28697200	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr6:28696000-28697400	Active TSS	Muscle Satellite Cultured Cells	--
25	chr6:28696000-28697400	Active TSS	Hela-S3	cervix
26	chr6:28696000-28697600	Active TSS	HSMMtube	muscle
27	chr6:28696000-28697600	Active TSS	NHEK	skin
28	chr6:28696000-28697600	Active TSS	Osteobl	bone
29	chr6:28696000-28697800	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr6:28696000-28698000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:28696000-28698000	Active TSS	HMEC	breast

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