Variant report

Variant	rs9353323
Chromosome Location	chr6:86339305-86339306
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:86337289-86339358	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86338689..86357756-chr6:86378394..86390434,115	MCF-7	breast:
2	chr6:86326728..86328514-chr6:86337033..86340056,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236016	TF binding region
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12528808	0.81[AFR][1000 genomes];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	0.92[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	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6913634	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6923017	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930543	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6930790	0.87[ASN][1000 genomes]
rs73751215	0.81[ASN][1000 genomes]
rs7744309	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7749600	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752105	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7757466	0.83[AFR][1000 genomes]
rs7771187	0.81[ASN][1000 genomes]
rs7771366	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7775788	0.98[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	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9351063	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9351066	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9353319	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9353321	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9353324	0.89[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	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444353	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444356	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450286	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9450289	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450294	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450295	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450299	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9450300	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450304	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450307	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450308	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450309	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450313	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv5383	chr6:86303223-86348023	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9353323	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs9353323	NT5E	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86313400-86349000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr6:86313800-86340200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:86314200-86341200	Strong transcription	HMEC	breast
4	chr6:86314800-86348600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:86315000-86347800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:86315400-86347400	Strong transcription	HUVEC	blood vessel
7	chr6:86316000-86348600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:86316200-86347800	Strong transcription	Duodenum Mucosa	Duodenum
9	chr6:86316200-86348600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr6:86316200-86348600	Strong transcription	Placenta	Placenta
11	chr6:86316200-86348800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:86316400-86348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:86316400-86348400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:86316400-86349200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:86316400-86350600	Strong transcription	Fetal Thymus	thymus
16	chr6:86317000-86340400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:86317000-86349000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:86317400-86349000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:86317600-86349800	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr6:86317800-86348200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:86318600-86348800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr6:86318800-86347200	Strong transcription	Fetal Brain Female	brain
23	chr6:86319000-86350000	Strong transcription	Fetal Muscle Trunk	muscle
24	chr6:86319400-86348600	Strong transcription	K562	blood
25	chr6:86319600-86342400	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr6:86319600-86348200	Strong transcription	NHEK	skin
27	chr6:86319600-86348800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:86319600-86350000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr6:86320000-86344200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:86320000-86348600	Strong transcription	Liver	Liver
31	chr6:86320200-86342400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:86320200-86350400	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr6:86321000-86348600	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:86321000-86349600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:86321200-86341200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:86323600-86349000	Strong transcription	Fetal Intestine Large	intestine
37	chr6:86323600-86351200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:86324800-86341400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr6:86324800-86348600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:86325400-86347000	Strong transcription	Hela-S3	cervix
41	chr6:86325600-86341200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:86326400-86349200	Strong transcription	Primary hematopoietic stem cells	blood
43	chr6:86328000-86349800	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:86330400-86342400	Weak transcription	Pancreas	Pancrea
45	chr6:86331400-86341200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:86331400-86348400	Strong transcription	NHDF-Ad	bronchial
47	chr6:86331400-86349000	Strong transcription	HSMM	muscle
48	chr6:86331600-86347400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:86331800-86347600	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr6:86332200-86346600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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