Variant report

Variant	rs12664908
Chromosome Location	chr6:86178662-86178663
allele	C/G/T
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	chr6:86177892-86178676	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86165562..86167766-chr6:86176895..86178725,2	MCF-7	breast:

Variant related genes	Relation type
NT5E	TF binding region

Extended variants
information (count: 169 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs1000632	0.90[ASN][1000 genomes]
rs1000633	0.90[ASN][1000 genomes]
rs1000634	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11508041	0.91[ASN][1000 genomes]
rs11963844	0.91[ASN][1000 genomes]
rs11968230	0.91[ASN][1000 genomes]
rs11968238	0.91[ASN][1000 genomes]
rs12055597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12524836	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12528808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12662033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[ASN][1000 genomes]
rs1322401	0.90[ASN][1000 genomes]
rs1322403	0.82[ASN][1000 genomes]
rs1322404	0.82[ASN][1000 genomes]
rs1570310	0.90[ASN][1000 genomes]
rs1570311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs1590279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1590280	0.88[ASN][1000 genomes]
rs1665786	0.82[ASN][1000 genomes]
rs1744121	0.82[ASN][1000 genomes]
rs1744122	0.82[ASN][1000 genomes]
rs2208722	0.90[ASN][1000 genomes]
rs2229524	0.90[ASN][1000 genomes]
rs2295890	0.91[ASN][1000 genomes]
rs3812137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3812139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4144166	0.97[ASN][1000 genomes]
rs4144167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4327657	0.90[ASN][1000 genomes]
rs4373339	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4400191	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4458647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4463232	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4487548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs4565270	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4571538	0.91[ASN][1000 genomes]
rs4624841	0.82[ASN][1000 genomes]
rs490079	0.82[ASN][1000 genomes]
rs494562	0.82[ASN][1000 genomes]
rs494688	0.85[JPT][hapmap]
rs495469	0.82[ASN][1000 genomes]
rs495472	0.82[ASN][1000 genomes]
rs498289	0.82[ASN][1000 genomes]
rs515980	0.82[ASN][1000 genomes]
rs520090	0.82[ASN][1000 genomes]
rs521005	0.82[ASN][1000 genomes]
rs522129	0.82[ASN][1000 genomes]
rs522915	0.82[ASN][1000 genomes]
rs527670	0.82[ASN][1000 genomes]
rs543359	0.82[ASN][1000 genomes]
rs544403	0.82[ASN][1000 genomes]
rs544408	0.82[ASN][1000 genomes]
rs547052	0.82[ASN][1000 genomes]
rs547963	0.82[ASN][1000 genomes]
rs550499	0.82[ASN][1000 genomes]
rs554113	0.82[ASN][1000 genomes]
rs567686	0.82[ASN][1000 genomes]
rs573737	0.82[ASN][1000 genomes]
rs573892	0.82[ASN][1000 genomes]
rs575477	0.82[ASN][1000 genomes]
rs589255	0.82[ASN][1000 genomes]
rs59797285	0.91[ASN][1000 genomes]
rs617483	0.82[ASN][1000 genomes]
rs618448	0.82[ASN][1000 genomes]
rs619299	0.82[ASN][1000 genomes]
rs619753	0.82[ASN][1000 genomes]
rs632163	0.82[ASN][1000 genomes]
rs637346	0.82[ASN][1000 genomes]
rs638745	0.82[ASN][1000 genomes]
rs640093	0.82[ASN][1000 genomes]
rs683218	0.82[ASN][1000 genomes]
rs6900270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6902638	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6902904	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6910543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6913634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6919207	0.82[ASN][1000 genomes]
rs6930790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6942065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs73751215	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7744309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7745560	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7746186	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7749600	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7749745	0.90[ASN][1000 genomes]
rs7750970	0.82[ASN][1000 genomes]
rs7752105	0.84[ASN][1000 genomes]
rs7753022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs7753711	0.82[ASN][1000 genomes]
rs7753936	0.90[ASN][1000 genomes]
rs7753950	0.90[ASN][1000 genomes]
rs7754559	0.90[ASN][1000 genomes]
rs7763191	0.82[ASN][1000 genomes]
rs7767626	0.82[ASN][1000 genomes]
rs7767800	0.82[ASN][1000 genomes]
rs7771187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7771366	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7771860	0.82[ASN][1000 genomes]
rs7772233	0.91[ASN][1000 genomes]
rs9294335	0.82[ASN][1000 genomes]
rs9294336	0.91[ASN][1000 genomes]
rs9342039	0.91[ASN][1000 genomes]
rs9344518	0.82[ASN][1000 genomes]
rs9344519	0.90[ASN][1000 genomes]
rs9344520	0.90[ASN][1000 genomes]
rs9344521	0.90[ASN][1000 genomes]
rs9344522	0.90[ASN][1000 genomes]
rs9344523	0.91[ASN][1000 genomes]
rs9344524	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9344525	0.91[ASN][1000 genomes]
rs9344526	0.91[ASN][1000 genomes]
rs9344527	0.97[ASN][1000 genomes]
rs9344528	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs9344529	0.97[ASN][1000 genomes]
rs9344530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9344538	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9351063	0.84[ASN][1000 genomes]
rs9353309	0.82[ASN][1000 genomes]
rs9353310	0.82[ASN][1000 genomes]
rs9353312	0.91[ASN][1000 genomes]
rs9353313	0.91[ASN][1000 genomes]
rs9353314	0.91[ASN][1000 genomes]
rs9353315	0.91[ASN][1000 genomes]
rs9353316	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9353317	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9353319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9353321	0.84[ASN][1000 genomes]
rs9353324	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9359654	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9359655	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[ASN][1000 genomes]
rs9359656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9362211	0.90[ASN][1000 genomes]
rs9362212	0.88[ASN][1000 genomes]
rs9362213	0.90[ASN][1000 genomes]
rs9362214	0.88[ASN][1000 genomes]
rs9362215	0.90[ASN][1000 genomes]
rs9362216	0.91[ASN][1000 genomes]
rs9362217	0.91[ASN][1000 genomes]
rs9362218	0.91[ASN][1000 genomes]
rs9362219	0.91[ASN][1000 genomes]
rs9362220	0.91[ASN][1000 genomes]
rs9362221	0.91[ASN][1000 genomes]
rs9362223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9362224	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9362225	0.90[ASN][1000 genomes]
rs9362226	0.84[ASN][1000 genomes]
rs9444342	0.88[ASN][1000 genomes]
rs9444343	0.88[ASN][1000 genomes]
rs9444353	0.84[ASN][1000 genomes]
rs9450274	0.91[ASN][1000 genomes]
rs9450278	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9450279	0.91[ASN][1000 genomes]
rs9450280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9450286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450289	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9450294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9450295	0.84[ASN][1000 genomes]
rs9450300	0.84[ASN][1000 genomes]
rs9450307	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9450308	1.00[CHB][hapmap];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12664908	NT5E	cis	Thyroid	GTEx
rs12664908	NT5E	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86171800-86185200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr6:86171800-86186000	Weak transcription	Fetal Stomach	stomach
3	chr6:86171800-86187600	Weak transcription	Colonic Mucosa	Colon
4	chr6:86172000-86179000	Weak transcription	Pancreas	Pancrea
5	chr6:86172200-86179800	Weak transcription	Left Ventricle	heart
6	chr6:86172200-86186000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:86172400-86192800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:86174600-86180200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:86174800-86179800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:86174800-86180400	Weak transcription	Brain Anterior Caudate	brain
11	chr6:86175000-86180000	Genic enhancers	HSMM	muscle
12	chr6:86175200-86180000	Genic enhancers	Muscle Satellite Cultured Cells	--
13	chr6:86175400-86180000	Genic enhancers	NHEK	skin
14	chr6:86175400-86180200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:86175400-86180200	Genic enhancers	NHLF	lung
16	chr6:86175600-86191800	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:86176000-86179000	Weak transcription	Lung	lung
18	chr6:86176000-86180600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:86176000-86183800	Genic enhancers	NHDF-Ad	bronchial
20	chr6:86176200-86179200	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:86176200-86183000	Weak transcription	Primary T cells from cord blood	blood
22	chr6:86176200-86187000	Strong transcription	Liver	Liver
23	chr6:86176200-86192400	Weak transcription	A549	lung
24	chr6:86176200-86192600	Weak transcription	HepG2	liver
25	chr6:86176400-86179400	Weak transcription	Spleen	Spleen
26	chr6:86176600-86191400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:86176800-86242600	Weak transcription	Gastric	stomach
28	chr6:86177600-86182200	Enhancers	Placenta	Placenta
29	chr6:86177800-86178800	Enhancers	Fetal Muscle Trunk	muscle
30	chr6:86177800-86179600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:86177800-86179800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:86177800-86180000	Genic enhancers	HMEC	breast
33	chr6:86177800-86180200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:86177800-86180400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:86177800-86180600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:86178000-86179200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:86178000-86179600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:86178000-86179600	Enhancers	Hela-S3	cervix
39	chr6:86178000-86180000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:86178000-86180200	Enhancers	HSMMtube	muscle
41	chr6:86178000-86180400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:86178000-86180400	Genic enhancers	Fetal Muscle Leg	muscle
43	chr6:86178000-86183800	Genic enhancers	Osteobl	bone
44	chr6:86178200-86178800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:86178200-86178800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:86178400-86179000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:86178400-86179400	Weak transcription	Ovary	ovary
48	chr6:86178400-86179600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:86178400-86181600	Weak transcription	Aorta	Aorta
50	chr6:86178600-86179200	Weak transcription	NH-A	brain

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