Variant report

Variant	rs1885690
Chromosome Location	chr6:109672998-109672999
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109668456..109674736-chr6:109696300..109702886,9	K562	blood:
2	chr6:109669515..109674044-chr6:109702916..109706265,4	K562	blood:
3	chr6:109660514..109663248-chr6:109671174..109674117,2	K562	blood:
4	chr6:109665458..109673633-chr6:109699710..109704931,12	MCF-7	breast:
5	chr6:109669396..109675577-chr6:109699158..109705270,9	K562	blood:
6	chr6:109669590..109673452-chr6:109701898..109703889,4	MCF-7	breast:
7	chr6:109667528..109670285-chr6:109670801..109673728,2	K562	blood:

Variant related genes	Relation type
ENSG00000135535	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1046943	0.86[EUR][1000 genomes]
rs1074765	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1074766	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10872033	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11251	0.95[EUR][1000 genomes]
rs12214147	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12529733	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13219952	0.93[EUR][1000 genomes]
rs1476387	0.93[EUR][1000 genomes]
rs1521907	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17070591	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1853330	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1885691	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2211288	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236084	0.86[EUR][1000 genomes]
rs2277113	0.88[EUR][1000 genomes]
rs2884037	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35146243	0.86[EUR][1000 genomes]
rs3734652	0.86[EUR][1000 genomes]
rs3757230	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757231	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757235	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778474	0.95[EUR][1000 genomes]
rs3778478	0.86[EUR][1000 genomes]
rs3818933	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4636056	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4945831	0.93[EUR][1000 genomes]
rs4946967	0.95[EUR][1000 genomes]
rs4946970	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4946976	0.88[EUR][1000 genomes]
rs58644322	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59597139	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6914216	0.92[EUR][1000 genomes]
rs6920372	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6939548	0.86[EUR][1000 genomes]
rs6939953	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs699700	0.95[EUR][1000 genomes]
rs730089	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs736830	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs746794	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7748669	0.90[EUR][1000 genomes]
rs7751582	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7754650	0.92[EUR][1000 genomes]
rs7768973	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8465	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs910730	0.89[EUR][1000 genomes]
rs9320286	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9372213	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9386799	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9480947	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9480949	0.91[EUR][1000 genomes]
rs9480956	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9480958	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9487064	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487066	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487069	0.95[EUR][1000 genomes]
rs9487070	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487076	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487084	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9487085	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9487103	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs974034	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9791241	0.86[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1885690	RP11-425D10.10	cis	Whole Blood	GTEx
rs1885690	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs1885690	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs1885690	SMPD2	cis	Esophagus Mucosa	GTEx
rs1885690	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 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	chr6:109654200-109675000	Weak transcription	Primary B cells from peripheral blood	blood
3	chr6:109654200-109676200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:109658800-109677000	Weak transcription	Fetal Stomach	stomach
5	chr6:109660200-109677200	Weak transcription	Thymus	Thymus
6	chr6:109660400-109674600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:109662600-109682000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:109662800-109677000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:109665600-109677000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:109665600-109680400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:109666000-109678000	Weak transcription	Fetal Kidney	kidney
12	chr6:109666400-109675200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr6:109668000-109673800	Enhancers	Stomach Mucosa	stomach
14	chr6:109668000-109674000	Enhancers	Fetal Intestine Large	intestine
15	chr6:109668000-109674600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:109668600-109674800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr6:109669000-109674000	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr6:109669000-109683400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:109669400-109673800	Enhancers	Colonic Mucosa	Colon
20	chr6:109669600-109677000	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:109669600-109677200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:109669800-109677200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:109670200-109673000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr6:109670400-109673200	Enhancers	Primary hematopoietic stem cells	blood
25	chr6:109670400-109674000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:109670600-109673200	Enhancers	Pancreas	Pancrea
27	chr6:109670800-109674400	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr6:109671000-109673600	Enhancers	Gastric	stomach
29	chr6:109671000-109677800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:109671000-109681600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr6:109671200-109677000	Weak transcription	Aorta	Aorta
32	chr6:109671200-109677200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:109671200-109680200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:109671200-109681400	Weak transcription	Brain Anterior Caudate	brain
35	chr6:109671400-109673000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:109671400-109674400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:109671400-109675000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:109671400-109675000	Weak transcription	Liver	Liver
39	chr6:109671400-109675000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:109671400-109675200	Weak transcription	Ovary	ovary
41	chr6:109671400-109675400	Weak transcription	Osteobl	bone
42	chr6:109671400-109675600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr6:109671400-109677200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:109671400-109677200	Weak transcription	A549	lung
45	chr6:109671400-109677600	Weak transcription	HepG2	liver
46	chr6:109671400-109677800	Weak transcription	Fetal Lung	lung
47	chr6:109671600-109673000	Weak transcription	Brain Substantia Nigra	brain
48	chr6:109671600-109673000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr6:109671600-109673200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:109671600-109674000	Enhancers	K562	blood

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