Variant report

Variant	rs6939953
Chromosome Location	chr6:109711319-109711320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109710996..109712933-chr6:109713290..109714925,2	MCF-7	breast:
2	chr6:109701817..109708859-chr6:109709273..109715844,12	K562	blood:
3	chr6:109711182..109714084-chr6:109716397..109718567,2	K562	blood:
4	chr6:109703167..109707934-chr6:109708161..109712915,9	MCF-7	breast:
5	chr6:109618104..109620663-chr6:109710406..109712166,2	MCF-7	breast:
6	chr6:109556764..109558719-chr6:109710608..109712276,2	K562	blood:

Variant related genes	Relation type
ENSG00000260273	Chromatin interaction
ENSG00000243587	Chromatin interaction
ENSG00000135535	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	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1074766	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10872033	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11251	0.94[EUR][1000 genomes]
rs12214147	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12529733	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13219952	0.95[EUR][1000 genomes]
rs1476387	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1521907	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17070591	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1853330	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1885690	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1885691	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2211288	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236084	0.86[EUR][1000 genomes]
rs2277113	0.88[EUR][1000 genomes]
rs2884037	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35146243	0.86[EUR][1000 genomes]
rs3734652	0.86[EUR][1000 genomes]
rs3757230	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757231	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757235	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778474	0.94[EUR][1000 genomes]
rs3778478	0.86[EUR][1000 genomes]
rs3818933	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4636056	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4945831	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4946967	0.94[EUR][1000 genomes]
rs4946970	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4946976	0.88[EUR][1000 genomes]
rs58644322	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59597139	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6914216	0.94[EUR][1000 genomes]
rs6920372	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6939548	0.86[EUR][1000 genomes]
rs699700	0.94[EUR][1000 genomes]
rs730089	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs736830	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs746794	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7748669	0.92[EUR][1000 genomes]
rs7751582	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7754650	0.94[EUR][1000 genomes]
rs7768973	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8465	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs910730	0.89[EUR][1000 genomes]
rs9320286	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9372213	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9386799	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9480947	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9480949	0.93[EUR][1000 genomes]
rs9480956	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9480958	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9487064	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487066	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487069	0.94[EUR][1000 genomes]
rs9487070	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9487076	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9487084	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487085	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487103	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs974034	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9791241	0.86[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6939953	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs6939953	SMPD2	cis	Esophagus Mucosa	GTEx
rs6939953	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs6939953	RP11-425D10.10	cis	Whole Blood	GTEx
rs6939953	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109705000-109745200	Weak transcription	Fetal Kidney	kidney
2	chr6:109706000-109711600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:109706200-109711600	Weak transcription	Fetal Lung	lung
4	chr6:109706200-109711800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr6:109706200-109717200	Weak transcription	Brain Angular Gyrus	brain
6	chr6:109706200-109717800	Weak transcription	Thymus	Thymus
7	chr6:109706400-109711400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:109706400-109715000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:109706400-109718400	Weak transcription	Primary B cells from cord blood	blood
10	chr6:109706600-109711400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:109706600-109711600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:109706600-109711600	Weak transcription	Fetal Stomach	stomach
13	chr6:109706600-109714800	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:109706600-109717400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:109706600-109735800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:109706800-109711400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr6:109706800-109711600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:109706800-109711600	Weak transcription	Pancreas	Pancrea
19	chr6:109706800-109711600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:109706800-109712600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:109706800-109715600	Weak transcription	Gastric	stomach
22	chr6:109706800-109718600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:109707000-109711600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr6:109707000-109712000	Weak transcription	Hela-S3	cervix
25	chr6:109707000-109755400	Weak transcription	Fetal Intestine Small	intestine
26	chr6:109709800-109714800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:109710200-109713400	Enhancers	Fetal Intestine Large	intestine
28	chr6:109710200-109714800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:109710600-109711400	Enhancers	HMEC	breast
30	chr6:109710600-109711600	Enhancers	Muscle Satellite Cultured Cells	--
31	chr6:109710800-109711400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:109710800-109711400	Enhancers	Brain Substantia Nigra	brain
33	chr6:109710800-109711600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:109710800-109711600	Enhancers	Aorta	Aorta
35	chr6:109710800-109711800	Enhancers	Left Ventricle	heart
36	chr6:109710800-109712000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:109710800-109712000	Enhancers	Stomach Mucosa	stomach
38	chr6:109710800-109712800	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr6:109710800-109712800	Enhancers	Adipose Nuclei	Adipose
40	chr6:109710800-109712800	Enhancers	Placenta	Placenta
41	chr6:109710800-109713000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:109710800-109713000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:109710800-109713000	Enhancers	NHEK	skin
44	chr6:109710800-109713200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:109711000-109711400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:109711000-109711600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr6:109711000-109711800	Enhancers	Primary T cells from cord blood	blood
48	chr6:109711000-109711800	Enhancers	Brain Anterior Caudate	brain
49	chr6:109711000-109711800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:109711000-109711800	Weak transcription	Osteobl	bone

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