Variant report

Variant	rs6923017
Chromosome Location	chr6:86302337-86302338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr6:86301986-86304867	SK-N-SH	brain:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:86252970..86257934-chr6:86299533..86304034,5	K562	blood:
2	chr6:86299824..86305374-chr6:86350530..86356322,11	MCF-7	breast:
3	chr16:89630470..89633084-chr6:86301680..86303446,2	MCF-7	breast:
4	chr6:86301331..86304881-chr6:86350851..86355985,12	MCF-7	breast:
5	chr6:86298683..86300956-chr6:86302311..86304856,2	MCF-7	breast:
6	chr6:86300286..86310605-chr6:86384413..86390498,39	K562	blood:
7	chr6:86299850..86302872-chr6:86358961..86362964,3	K562	blood:
8	chr6:86191399..86193392-chr6:86300815..86302853,2	K562	blood:
9	chr6:86300457..86307827-chr6:86347697..86356337,20	K562	blood:
10	chr6:86301325..86305014-chr6:86385299..86388840,4	MCF-7	breast:
11	chr6:86302271..86307129-chr6:86385631..86390073,11	MCF-7	breast:
12	chr6:86300873..86305245-chr6:86347697..86356641,19	K562	blood:
13	chr6:86284643..86286706-chr6:86299863..86303229,3	K562	blood:
14	chr6:86298349..86307534-chr6:86383938..86391964,31	K562	blood:
15	chr6:86298806..86300763-chr6:86301374..86304077,2	MCF-7	breast:

No data

Variant related genes	Relation type
SNX14	TF binding region
ENSG00000135316	Chromatin interaction
ENSG00000203875	Chromatin interaction
ENSG00000135317	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12528808	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2229524	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3812137	0.81[ASN][1000 genomes]
rs3812139	0.81[ASN][1000 genomes]
rs4327657	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59744370	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6900270	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6902638	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902904	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6910543	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6913634	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6930543	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6930790	0.87[ASN][1000 genomes]
rs73751215	0.81[ASN][1000 genomes]
rs7744309	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7749600	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752105	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7757466	0.80[AFR][1000 genomes]
rs7771187	0.81[ASN][1000 genomes]
rs7771366	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7775788	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344530	0.81[ASN][1000 genomes]
rs9344538	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9351063	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9351066	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9353319	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9353321	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9353323	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9353324	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9362223	0.81[ASN][1000 genomes]
rs9362225	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9362226	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444353	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444356	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450286	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9450289	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450294	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450295	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450299	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9450300	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450304	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450307	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450308	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450309	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450313	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
4	esv1792638	chr6:86224053-86336300	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv3351743	chr6:86286282-86308720	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6923017	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs6923017	NT5E	cis	Thyroid	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86224200-86302600	Weak transcription	Colonic Mucosa	Colon
2	chr6:86278200-86302600	Weak transcription	Ovary	ovary
3	chr6:86290400-86302400	Weak transcription	Placenta	Placenta
4	chr6:86291000-86302600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:86291200-86302600	Weak transcription	Pancreas	Pancrea
6	chr6:86291200-86302600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:86291200-86302800	Weak transcription	Gastric	stomach
8	chr6:86297800-86302600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:86298600-86302400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:86298800-86302600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:86299400-86302600	Weak transcription	Spleen	Spleen
12	chr6:86300400-86302600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr6:86300600-86302600	Enhancers	Primary B cells from peripheral blood	blood
14	chr6:86300600-86302600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:86300600-86302600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr6:86300600-86302600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr6:86301000-86302600	Enhancers	Primary B cells from cord blood	blood
18	chr6:86301000-86302600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr6:86301000-86302600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr6:86301200-86302400	Enhancers	Fetal Lung	lung
21	chr6:86301200-86302600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:86301200-86302600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:86301200-86302600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:86301200-86302600	Enhancers	Adipose Nuclei	Adipose
25	chr6:86301200-86302600	Enhancers	Brain Substantia Nigra	brain
26	chr6:86301400-86302400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:86301400-86302400	Enhancers	Thymus	Thymus
28	chr6:86301400-86302600	Enhancers	Primary T cells fromperipheralblood	blood
29	chr6:86301400-86302600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:86301600-86302400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:86301600-86302400	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:86301600-86302400	Enhancers	Fetal Thymus	thymus
33	chr6:86301600-86302600	Weak transcription	Aorta	Aorta
34	chr6:86301600-86302600	Enhancers	Small Intestine	intestine
35	chr6:86301600-86303600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:86301800-86302400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:86301800-86302400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:86301800-86302400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr6:86301800-86302400	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr6:86301800-86302400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr6:86301800-86302400	Flanking Active TSS	Fetal Brain Male	brain
42	chr6:86301800-86302400	Enhancers	Fetal Intestine Large	intestine
43	chr6:86301800-86302400	Weak transcription	Left Ventricle	heart
44	chr6:86301800-86302400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr6:86301800-86302400	Flanking Active TSS	GM12878-XiMat	blood
46	chr6:86301800-86302600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:86301800-86302600	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr6:86301800-86302600	Enhancers	Primary hematopoietic stem cells	blood
49	chr6:86301800-86302600	Weak transcription	Psoas Muscle	Psoas
50	chr6:86301800-86302600	Enhancers	Skeletal Muscle Male	skeletal muscle

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