Variant report

Variant	rs9344529
Chromosome Location	chr6:86165542-86165543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86159096..86161442-chr6:86164229..86167917,3	MCF-7	breast:
2	chr6:86160188..86163833-chr6:86163850..86166659,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135318	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs1000632	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1000633	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1000634	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11508041	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11963844	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11968230	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11968238	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12055597	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12524836	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12528808	0.87[ASN][1000 genomes]
rs12662033	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12664908	0.97[ASN][1000 genomes]
rs1322401	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1322403	0.84[ASN][1000 genomes]
rs1322404	0.84[ASN][1000 genomes]
rs1570310	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1570311	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1590279	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1590280	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1665786	0.84[ASN][1000 genomes]
rs1744121	0.84[ASN][1000 genomes]
rs1744122	0.84[ASN][1000 genomes]
rs2208722	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2229524	0.87[ASN][1000 genomes]
rs2295890	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812137	0.87[ASN][1000 genomes]
rs3812139	0.87[ASN][1000 genomes]
rs4144166	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144167	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4327657	0.87[ASN][1000 genomes]
rs4373339	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4400191	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4458647	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4463232	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4487548	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4565270	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4571538	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4624841	0.84[ASN][1000 genomes]
rs490079	0.84[ASN][1000 genomes]
rs494562	0.84[ASN][1000 genomes]
rs495469	0.84[ASN][1000 genomes]
rs495472	0.84[ASN][1000 genomes]
rs498289	0.84[ASN][1000 genomes]
rs515980	0.84[ASN][1000 genomes]
rs520090	0.84[ASN][1000 genomes]
rs521005	0.84[ASN][1000 genomes]
rs522129	0.84[ASN][1000 genomes]
rs522915	0.84[ASN][1000 genomes]
rs527670	0.84[ASN][1000 genomes]
rs543359	0.84[ASN][1000 genomes]
rs544403	0.84[ASN][1000 genomes]
rs544408	0.84[ASN][1000 genomes]
rs547052	0.84[ASN][1000 genomes]
rs547963	0.84[ASN][1000 genomes]
rs550499	0.84[ASN][1000 genomes]
rs554113	0.84[ASN][1000 genomes]
rs567686	0.84[ASN][1000 genomes]
rs573737	0.84[ASN][1000 genomes]
rs573892	0.84[ASN][1000 genomes]
rs575477	0.84[ASN][1000 genomes]
rs589255	0.84[ASN][1000 genomes]
rs59797285	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs617483	0.84[ASN][1000 genomes]
rs618448	0.84[ASN][1000 genomes]
rs619299	0.84[ASN][1000 genomes]
rs619753	0.84[ASN][1000 genomes]
rs632163	0.84[ASN][1000 genomes]
rs637346	0.84[ASN][1000 genomes]
rs638745	0.84[ASN][1000 genomes]
rs640093	0.84[ASN][1000 genomes]
rs683218	0.84[ASN][1000 genomes]
rs6900270	0.87[ASN][1000 genomes]
rs6902904	0.87[ASN][1000 genomes]
rs6910543	0.81[ASN][1000 genomes]
rs6913634	0.87[ASN][1000 genomes]
rs6919207	0.84[ASN][1000 genomes]
rs6930790	0.81[ASN][1000 genomes]
rs6942065	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73751215	0.87[ASN][1000 genomes]
rs7744309	0.81[ASN][1000 genomes]
rs7746186	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749745	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7750970	0.84[ASN][1000 genomes]
rs7752105	0.81[ASN][1000 genomes]
rs7753022	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7753711	0.84[ASN][1000 genomes]
rs7753936	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7753950	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7754559	0.88[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7763191	0.84[ASN][1000 genomes]
rs7767626	0.84[ASN][1000 genomes]
rs7767800	0.84[ASN][1000 genomes]
rs7771187	0.87[ASN][1000 genomes]
rs7771860	0.84[ASN][1000 genomes]
rs7772233	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9294335	0.84[ASN][1000 genomes]
rs9294336	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9342039	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9344518	0.84[ASN][1000 genomes]
rs9344519	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9344520	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9344521	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9344522	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9344523	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9344524	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9344525	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9344526	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9344527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344528	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344530	0.87[ASN][1000 genomes]
rs9351063	0.81[ASN][1000 genomes]
rs9353309	0.84[ASN][1000 genomes]
rs9353310	0.84[ASN][1000 genomes]
rs9353312	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9353313	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9353314	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9353315	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9353316	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9353317	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9353319	0.81[ASN][1000 genomes]
rs9353321	0.81[ASN][1000 genomes]
rs9359654	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9359655	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9359656	0.93[ASN][1000 genomes]
rs9362211	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9362212	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9362213	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9362214	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9362215	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9362216	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9362217	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9362218	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9362219	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9362220	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9362221	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9362223	0.87[ASN][1000 genomes]
rs9362224	0.87[ASN][1000 genomes]
rs9362225	0.87[ASN][1000 genomes]
rs9362226	0.81[ASN][1000 genomes]
rs9444342	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9444343	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9444346	0.80[EUR][1000 genomes]
rs9444353	0.81[ASN][1000 genomes]
rs9450271	0.81[ASN][1000 genomes]
rs9450274	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450278	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450279	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450280	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450286	0.87[ASN][1000 genomes]
rs9450289	0.81[ASN][1000 genomes]
rs9450294	0.81[ASN][1000 genomes]
rs9450295	0.81[ASN][1000 genomes]
rs9450300	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv520112	chr6:86144875-86247759	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9344529	NT5E	cis	Whole Blood	GTEx
rs9344529	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs9344529	NT5E	cis	Thyroid	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86160600-86168000	Weak transcription	Lung	lung
2	chr6:86160600-86171400	Weak transcription	Gastric	stomach
3	chr6:86160800-86167000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:86160800-86168000	Weak transcription	Esophagus	oesophagus
5	chr6:86161200-86168600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:86161600-86167000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:86161800-86166400	Weak transcription	Right Atrium	heart
8	chr6:86161800-86167600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:86161800-86170400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:86162000-86166400	Weak transcription	Brain Anterior Caudate	brain
11	chr6:86162800-86172600	Enhancers	Liver	Liver
12	chr6:86163000-86166200	Weak transcription	Hela-S3	cervix
13	chr6:86163000-86166600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:86163000-86167600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:86163000-86167800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:86163200-86167000	Weak transcription	HSMMtube	muscle
17	chr6:86163200-86176600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr6:86163400-86166400	Enhancers	HepG2	liver
19	chr6:86163400-86167800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:86163400-86168200	Weak transcription	Fetal Stomach	stomach
21	chr6:86163400-86170600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:86163600-86166000	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:86163600-86167000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:86163600-86167400	Weak transcription	NH-A	brain
25	chr6:86163600-86167800	Weak transcription	A549	lung
26	chr6:86163600-86168000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:86163600-86168200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:86163600-86170400	Weak transcription	Spleen	Spleen
29	chr6:86163600-86171200	Weak transcription	Placenta	Placenta
30	chr6:86163800-86166800	Weak transcription	HUVEC	blood vessel
31	chr6:86163800-86167200	Genic enhancers	HMEC	breast
32	chr6:86163800-86167600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:86164000-86165800	Enhancers	NHLF	lung
34	chr6:86164000-86166000	Weak transcription	Ovary	ovary
35	chr6:86164000-86168000	Weak transcription	Aorta	Aorta
36	chr6:86164000-86168000	Weak transcription	Fetal Thymus	thymus
37	chr6:86164000-86169800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:86164000-86171200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr6:86164200-86167400	Weak transcription	Colon Smooth Muscle	Colon
40	chr6:86164200-86167600	Genic enhancers	Osteobl	bone
41	chr6:86164400-86166000	Flanking Active TSS	NHDF-Ad	bronchial
42	chr6:86164400-86167600	Weak transcription	Primary B cells from cord blood	blood
43	chr6:86164600-86167200	Genic enhancers	NHEK	skin
44	chr6:86164600-86168200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:86164800-86167200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:86164800-86168000	Weak transcription	Pancreas	Pancrea
47	chr6:86165000-86165800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
48	chr6:86165000-86165800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:86165000-86166400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:86165000-86166600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--

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