Variant report

Variant	rs9386799
Chromosome Location	chr6:109654601-109654602
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109649495..109651298-chr6:109651628..109654623,3	K562	blood:
2	chr6:109654193..109659063-chr6:109701671..109705275,8	MCF-7	breast:
3	chr6:109654230..109656152-chr6:109690482..109693249,2	MCF-7	breast:
4	chr6:109652681..109655937-chr6:109701274..109703936,3	MCF-7	breast:
5	chr6:109654487..109657351-chr6:109665508..109668370,2	K562	blood:
6	chr6:109652928..109655072-chr6:109655937..109657890,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260273	Chromatin interaction
ENSG00000135535	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1074765	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1074766	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11251	0.80[EUR][1000 genomes]
rs12529733	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1521907	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1853330	0.85[AMR][1000 genomes]
rs1885690	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1885691	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2211288	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2884037	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3757230	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3757231	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3757235	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3778474	0.80[EUR][1000 genomes]
rs3818933	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4946967	0.80[EUR][1000 genomes]
rs4946970	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58644322	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6920372	0.81[EUR][1000 genomes]
rs6939953	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs699700	0.80[EUR][1000 genomes]
rs730089	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs736830	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs746794	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8465	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9320286	0.81[EUR][1000 genomes]
rs9372213	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9398202	0.81[EUR][1000 genomes]
rs9480947	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9487064	0.85[EUR][1000 genomes]
rs9487066	0.83[EUR][1000 genomes]
rs9487069	0.80[EUR][1000 genomes]
rs9487070	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9487076	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9487084	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9487085	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs974034	0.86[AMR][1000 genomes];0.84[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	nsv5435	chr6:109633035-109669127	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9386799	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs9386799	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs9386799	MICAL1	cis	Artery Tibial	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109644600-109675200	Weak transcription	Primary T cells from cord blood	blood
2	chr6:109644800-109657400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:109645400-109662400	Weak transcription	Aorta	Aorta
4	chr6:109653000-109655000	Enhancers	Fetal Intestine Large	intestine
5	chr6:109653000-109655000	Enhancers	Fetal Intestine Small	intestine
6	chr6:109653000-109655000	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr6:109653400-109658800	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr6:109653800-109656400	Weak transcription	Colonic Mucosa	Colon
9	chr6:109654000-109657400	Weak transcription	Pancreas	Pancrea
10	chr6:109654000-109657600	Weak transcription	Adipose Nuclei	Adipose
11	chr6:109654000-109669400	Weak transcription	Small Intestine	intestine
12	chr6:109654200-109657000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr6:109654200-109657400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:109654200-109671000	Weak transcription	Spleen	Spleen
15	chr6:109654200-109675000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:109654200-109676200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:109654400-109656600	Weak transcription	Gastric	stomach
18	chr6:109654400-109657400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:109654400-109657400	Weak transcription	Placenta	Placenta
20	chr6:109654400-109657400	Weak transcription	Right Ventricle	heart
21	chr6:109654400-109657400	Weak transcription	Hela-S3	cervix
22	chr6:109654400-109657600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr6:109654400-109657600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:109654400-109657800	Weak transcription	K562	blood
25	chr6:109654400-109660600	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:109654400-109668800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr6:109654600-109655800	Weak transcription	Stomach Mucosa	stomach
28	chr6:109654600-109657400	Weak transcription	HepG2	liver

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