Variant report

Variant	rs12524836
Chromosome Location	chr6:86175956-86175957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1000632	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1000633	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1000634	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11508041	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11963844	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11968230	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11968238	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12055597	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12528808	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12662033	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12664908	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1322401	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1570310	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1570311	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1590279	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1590280	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2208722	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2229524	0.85[ASN][1000 genomes]
rs2295890	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3812137	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.85[ASN][1000 genomes]
rs3812139	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4144166	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4144167	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4327657	0.85[ASN][1000 genomes]
rs4373339	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4400191	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4458647	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4463232	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4487548	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4565270	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4571538	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59797285	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6900270	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs6902638	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6902904	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6910543	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6913634	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6930790	1.00[CHB][hapmap];0.92[YRI][hapmap]
rs6942065	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73751215	0.85[ASN][1000 genomes]
rs7744309	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7745560	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7746186	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7749600	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7749745	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7753022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7753936	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7753950	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7754559	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7771187	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7771366	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7772233	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9294336	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9342039	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344519	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344520	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344521	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344522	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344523	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344524	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344525	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344526	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344527	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9344528	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9344529	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9344530	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs9344538	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9353312	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9353313	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9353314	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9353315	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9353316	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9353317	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9353319	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9353324	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9359654	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9359655	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9359656	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9362211	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9362212	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9362213	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9362214	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9362215	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9362216	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9362217	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9362218	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9362219	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9362220	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9362221	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9362223	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9362224	0.85[ASN][1000 genomes]
rs9362225	0.85[ASN][1000 genomes]
rs9444342	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9444343	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9450274	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9450278	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9450279	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9450280	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9450286	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9450294	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9450307	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs9450308	1.00[CHB][hapmap];0.88[JPT][hapmap]

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
rs12524836	NT5E	cis	Whole Blood	GTEx
rs12524836	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs12524836	NT5E	cis	Thyroid	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86163200-86176600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr6:86167800-86176200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:86171800-86176800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:86171800-86185200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:86171800-86186000	Weak transcription	Fetal Stomach	stomach
6	chr6:86171800-86187600	Weak transcription	Colonic Mucosa	Colon
7	chr6:86172000-86179000	Weak transcription	Pancreas	Pancrea
8	chr6:86172200-86179800	Weak transcription	Left Ventricle	heart
9	chr6:86172200-86186000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:86172400-86176200	Enhancers	Primary T cells from cord blood	blood
11	chr6:86172400-86178000	Weak transcription	Aorta	Aorta
12	chr6:86172400-86192800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:86173200-86176200	Enhancers	GM12878-XiMat	blood
14	chr6:86173400-86176000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:86174000-86176600	Enhancers	Placenta	Placenta
16	chr6:86174200-86176000	Enhancers	Esophagus	oesophagus
17	chr6:86174200-86176200	Weak transcription	Liver	Liver
18	chr6:86174200-86177000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:86174400-86176000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr6:86174400-86176000	Weak transcription	Gastric	stomach
21	chr6:86174400-86176200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:86174400-86176200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:86174600-86176000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:86174600-86176000	Enhancers	HMEC	breast
25	chr6:86174600-86176200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:86174600-86178600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:86174600-86180200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:86174800-86176000	Enhancers	NHDF-Ad	bronchial
29	chr6:86174800-86176200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:86174800-86178000	Weak transcription	Fetal Muscle Leg	muscle
31	chr6:86174800-86179800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:86174800-86180400	Weak transcription	Brain Anterior Caudate	brain
33	chr6:86175000-86176000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:86175000-86176000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:86175000-86176200	Enhancers	A549	lung
36	chr6:86175000-86180000	Genic enhancers	HSMM	muscle
37	chr6:86175200-86176400	Enhancers	HUVEC	blood vessel
38	chr6:86175200-86180000	Genic enhancers	Muscle Satellite Cultured Cells	--
39	chr6:86175400-86176000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr6:86175400-86176000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:86175400-86176000	Enhancers	Lung	lung
42	chr6:86175400-86176200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
43	chr6:86175400-86176200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:86175400-86176400	Enhancers	Primary B cells from peripheral blood	blood
45	chr6:86175400-86180000	Genic enhancers	NHEK	skin
46	chr6:86175400-86180200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:86175400-86180200	Genic enhancers	NHLF	lung
48	chr6:86175600-86176200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr6:86175600-86176200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr6:86175600-86176600	Enhancers	Hela-S3	cervix

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