Variant report

Variant	rs313204
Chromosome Location	chr6:86114296-86114297
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1000632	0.84[ASN][1000 genomes]
rs1000633	0.84[ASN][1000 genomes]
rs1000634	0.84[ASN][1000 genomes]
rs12055597	0.84[ASN][1000 genomes]
rs1322401	0.84[ASN][1000 genomes]
rs1322403	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1322404	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1570310	0.84[ASN][1000 genomes]
rs1590279	0.82[ASN][1000 genomes]
rs1590280	0.82[ASN][1000 genomes]
rs1665786	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1744121	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1744122	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2208722	0.84[ASN][1000 genomes]
rs313206	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624841	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs490079	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs494562	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs494688	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs495469	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs495472	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs498289	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs515980	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs520090	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs521005	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs522129	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs522915	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs527670	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs543359	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs544403	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs544408	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs547052	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs547963	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs550499	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs554113	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs567686	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs573737	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs573892	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs575477	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs588823	0.97[AMR][1000 genomes]
rs589255	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs617483	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs618448	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs619299	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs619753	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs630212	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs632163	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs637346	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs638745	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs640093	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs643591	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683218	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6919207	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs693077	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727870	0.88[ASN][1000 genomes]
rs7749745	0.84[ASN][1000 genomes]
rs7750970	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7753711	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7753936	0.84[ASN][1000 genomes]
rs7753950	0.84[ASN][1000 genomes]
rs7754559	0.84[ASN][1000 genomes]
rs7763191	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7767626	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7767800	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7771860	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9294335	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9344518	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9344519	0.84[ASN][1000 genomes]
rs9344520	0.84[ASN][1000 genomes]
rs9344521	0.84[ASN][1000 genomes]
rs9344522	0.84[ASN][1000 genomes]
rs9353309	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9353310	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9362209	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9362211	0.84[ASN][1000 genomes]
rs9362212	0.82[ASN][1000 genomes]
rs9362213	0.84[ASN][1000 genomes]
rs9362214	0.82[ASN][1000 genomes]
rs9362215	0.84[ASN][1000 genomes]
rs9450260	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450263	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450269	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450270	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450271	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv830721	chr6:85987644-86147414	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	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
7	nsv1019960	chr6:86023236-86136666	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs313204	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs313204	NT5E	cis	Whole Blood	GTEx
rs313204	NT5E	cis	Thyroid	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86108400-86116600	Enhancers	Fetal Intestine Small	intestine
2	chr6:86110200-86115800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr6:86110200-86116000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:86110800-86116600	Enhancers	Fetal Intestine Large	intestine
5	chr6:86111000-86114600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr6:86111000-86115800	Enhancers	Primary T cells from cord blood	blood
7	chr6:86111000-86116200	Enhancers	Small Intestine	intestine
8	chr6:86111000-86116600	Enhancers	Placenta Amnion	Placenta Amnion
9	chr6:86111200-86114600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:86111200-86115200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr6:86111200-86116200	Enhancers	Stomach Mucosa	stomach
12	chr6:86111200-86116400	Enhancers	Placenta	Placenta
13	chr6:86111400-86115200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:86111400-86115600	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr6:86111600-86114400	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:86111600-86115000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:86111800-86115000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr6:86112000-86114600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr6:86112000-86114800	Weak transcription	Dnd41	blood
20	chr6:86112200-86114400	Weak transcription	Fetal Thymus	thymus
21	chr6:86112200-86114600	Weak transcription	GM12878-XiMat	blood
22	chr6:86112600-86114400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:86112600-86115400	Enhancers	Esophagus	oesophagus
24	chr6:86112800-86114400	Enhancers	Duodenum Mucosa	Duodenum
25	chr6:86112800-86114600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr6:86112800-86114600	Flanking Active TSS	NH-A	brain
27	chr6:86112800-86114800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr6:86112800-86115000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr6:86112800-86115600	Flanking Active TSS	NHEK	skin
30	chr6:86112800-86115800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr6:86113000-86114400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:86113000-86114600	Flanking Active TSS	Osteobl	bone
33	chr6:86113000-86115600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:86113000-86115600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:86113200-86114600	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr6:86113400-86114400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:86113400-86115400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:86113400-86115400	Weak transcription	Lung	lung
39	chr6:86113400-86115400	Weak transcription	Ovary	ovary
40	chr6:86113400-86131600	Weak transcription	Right Atrium	heart
41	chr6:86113600-86114400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:86113600-86114600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:86113600-86114600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:86113600-86115000	Weak transcription	Adipose Nuclei	Adipose
45	chr6:86113600-86115400	Enhancers	Liver	Liver
46	chr6:86113600-86115400	Flanking Active TSS	HUVEC	blood vessel
47	chr6:86113600-86115600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:86113800-86114400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:86113800-86114800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:86113800-86115000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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