Variant report

Variant	rs17757715
Chromosome Location	chr4:147110652-147110653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10000407	0.83[EUR][1000 genomes]
rs10519776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079476	0.98[ASN][1000 genomes]
rs11100919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721367	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721873	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723069	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11724307	0.85[EUR][1000 genomes]
rs11725678	0.81[EUR][1000 genomes]
rs11728525	0.85[EUR][1000 genomes]
rs11728609	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730306	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733347	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940961	0.81[EUR][1000 genomes]
rs12152657	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152692	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021186	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021217	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17756056	0.83[EUR][1000 genomes]
rs17756234	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17757522	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758092	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17758396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758420	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814065	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814598	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864371	0.81[EUR][1000 genomes]
rs1865531	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007366	0.83[EUR][1000 genomes]
rs2068009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115796	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115797	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164280	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28393640	0.81[EUR][1000 genomes]
rs28420466	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733458	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733459	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733460	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756081	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756082	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756083	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775498	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815967	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3948408	0.81[EUR][1000 genomes]
rs4282199	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549398	0.81[EUR][1000 genomes]
rs4835286	0.81[EUR][1000 genomes]
rs55736910	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56174047	0.85[EUR][1000 genomes]
rs56279747	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56289966	0.81[EUR][1000 genomes]
rs56333123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56393662	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62326764	0.81[EUR][1000 genomes]
rs62326797	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62326801	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326802	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326848	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537399	0.81[EUR][1000 genomes]
rs6537400	0.83[EUR][1000 genomes]
rs6537401	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537402	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537403	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815527	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820462	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821066	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821444	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821479	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821863	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824313	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832576	0.83[EUR][1000 genomes]
rs6838458	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6839123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856647	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6858813	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72727922	0.81[EUR][1000 genomes]
rs72727944	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72727952	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7657269	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665079	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695415	0.83[EUR][1000 genomes]
rs7745	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919482	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919483	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461674	chr4:147047072-147143572	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv595650	chr4:147047072-147143572	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1018859	chr4:147055618-147138397	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17757715	RP11-6L6.2	cis	Nerve Tibial	GTEx
rs17757715	RP11-6L6.2	cis	lung	GTEx
rs17757715	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs17757715	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147097800-147111000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:147097800-147115400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:147098400-147111400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:147098400-147118600	Weak transcription	Colonic Mucosa	Colon
5	chr4:147098600-147113800	Weak transcription	Hela-S3	cervix
6	chr4:147101400-147111400	Weak transcription	Right Ventricle	heart
7	chr4:147101400-147114000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr4:147101400-147116200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:147101600-147111200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:147101600-147111200	Weak transcription	Small Intestine	intestine
11	chr4:147102600-147113800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr4:147103600-147113400	Strong transcription	Primary hematopoietic stem cells	blood
13	chr4:147103600-147114000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr4:147103800-147111400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:147103800-147112800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:147103800-147113400	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr4:147103800-147113600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:147103800-147113600	Strong transcription	Primary B cells from cord blood	blood
19	chr4:147103800-147114000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:147103800-147114000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:147103800-147114200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:147103800-147117400	Strong transcription	Primary T cells from cord blood	blood
23	chr4:147104000-147111400	Weak transcription	Stomach Mucosa	stomach
24	chr4:147104000-147113000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:147104000-147113400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:147104000-147113600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr4:147104200-147111400	Strong transcription	Adipose Nuclei	Adipose
28	chr4:147104200-147112200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr4:147104200-147113200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:147104200-147113200	Strong transcription	Placenta	Placenta
31	chr4:147104200-147113800	Strong transcription	Fetal Thymus	thymus
32	chr4:147104200-147114200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr4:147104400-147112200	Strong transcription	Fetal Intestine Large	intestine
34	chr4:147104400-147113200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr4:147104400-147113800	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr4:147104400-147114000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr4:147104400-147114200	Strong transcription	Fetal Muscle Leg	muscle
38	chr4:147105000-147113400	Strong transcription	Liver	Liver
39	chr4:147105000-147113800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:147105200-147112800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:147105600-147111000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:147105600-147113800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:147105800-147111200	Weak transcription	Ovary	ovary
44	chr4:147105800-147113200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr4:147105800-147113800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:147106200-147111400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr4:147107200-147112400	Strong transcription	Dnd41	blood
48	chr4:147107200-147113000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:147107200-147113000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr4:147107400-147111400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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