Variant report

Variant	rs9487066
Chromosome Location	chr6:109668910-109668911
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109668456..109674736-chr6:109696300..109702886,9	K562	blood:
2	chr6:109629710..109632603-chr6:109666871..109669752,2	K562	blood:
3	chr6:109667528..109670285-chr6:109670801..109673728,2	K562	blood:
4	chr6:109666475..109669130-chr6:109690489..109693013,2	K562	blood:
5	chr6:109666918..109669416-chr6:109676939..109680789,3	MCF-7	breast:
6	chr6:109414928..109417329-chr6:109668805..109670563,2	K562	blood:
7	chr6:109665458..109673633-chr6:109699710..109704931,12	MCF-7	breast:
8	chr6:109667580..109670112-chr6:109691835..109693593,2	MCF-7	breast:
9	chr6:109665666..109669140-chr6:109702115..109705884,4	MCF-7	breast:
10	chr6:109659815..109666445-chr6:109666719..109672363,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000203799	Chromatin interaction
ENSG00000183137	Chromatin interaction
ENSG00000080546	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1074765	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1074766	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10872033	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11251	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12214147	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12529733	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13219952	0.91[EUR][1000 genomes]
rs1476387	0.86[EUR][1000 genomes]
rs1521907	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17070591	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1853330	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1885690	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1885691	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2211288	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277113	0.81[EUR][1000 genomes]
rs2884037	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757230	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757231	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757235	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778474	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3818933	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4636056	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4945831	0.86[EUR][1000 genomes]
rs4946967	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4946970	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4946976	0.81[EUR][1000 genomes]
rs58644322	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59597139	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6914216	0.90[EUR][1000 genomes]
rs6920372	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6939953	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs699700	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs730089	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs736830	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs746794	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7748669	0.88[EUR][1000 genomes]
rs7751582	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7754650	0.90[EUR][1000 genomes]
rs7768973	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8465	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs910730	0.82[EUR][1000 genomes]
rs9320286	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9372213	0.81[EUR][1000 genomes]
rs9386799	0.83[EUR][1000 genomes]
rs9480947	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9480949	0.89[EUR][1000 genomes]
rs9480956	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9480958	0.86[EUR][1000 genomes]
rs9487064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487069	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9487070	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9487076	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9487084	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9487085	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9487103	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs974034	0.92[EUR][1000 genomes];0.99[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9487066	SMPD2	cis	Whole Blood	GTEx
rs9487066	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs9487066	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs9487066	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs9487066	MICAL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109644600-109675200	Weak transcription	Primary T cells from cord blood	blood
2	chr6:109654000-109669400	Weak transcription	Small Intestine	intestine
3	chr6:109654200-109671000	Weak transcription	Spleen	Spleen
4	chr6:109654200-109675000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:109654200-109676200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:109657800-109671000	Weak transcription	Lung	lung
7	chr6:109658400-109669200	Weak transcription	Liver	Liver
8	chr6:109658600-109670600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:109658800-109670600	Weak transcription	Right Atrium	heart
10	chr6:109658800-109677000	Weak transcription	Fetal Stomach	stomach
11	chr6:109660200-109677200	Weak transcription	Thymus	Thymus
12	chr6:109660400-109674600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:109661400-109671400	Weak transcription	Fetal Thymus	thymus
14	chr6:109662600-109682000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:109662800-109669600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:109662800-109670600	Weak transcription	Aorta	Aorta
17	chr6:109662800-109670600	Weak transcription	Right Ventricle	heart
18	chr6:109662800-109671000	Weak transcription	Psoas Muscle	Psoas
19	chr6:109662800-109677000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:109663000-109670600	Weak transcription	Adipose Nuclei	Adipose
21	chr6:109664000-109669000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:109664000-109670800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:109664200-109669000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:109664200-109670800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:109664200-109672800	Weak transcription	HSMM	muscle
26	chr6:109664400-109670400	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr6:109664400-109670600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr6:109664400-109671000	Weak transcription	Left Ventricle	heart
29	chr6:109665200-109669000	Weak transcription	K562	blood
30	chr6:109665600-109669200	Weak transcription	Gastric	stomach
31	chr6:109665600-109670600	Weak transcription	Pancreas	Pancrea
32	chr6:109665600-109677000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:109665600-109680400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr6:109665800-109669000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:109665800-109669600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr6:109665800-109670600	Weak transcription	Fetal Muscle Leg	muscle
37	chr6:109666000-109669000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:109666000-109670800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:109666000-109678000	Weak transcription	Fetal Kidney	kidney
40	chr6:109666400-109669000	Weak transcription	Placenta	Placenta
41	chr6:109666400-109675200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr6:109667000-109669800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:109667800-109671400	Enhancers	Fetal Intestine Small	intestine
44	chr6:109668000-109669200	Enhancers	Brain Substantia Nigra	brain
45	chr6:109668000-109671200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr6:109668000-109673800	Enhancers	Stomach Mucosa	stomach
47	chr6:109668000-109674000	Enhancers	Fetal Intestine Large	intestine
48	chr6:109668000-109674600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:109668200-109669000	Enhancers	Colonic Mucosa	Colon
50	chr6:109668400-109669800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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