Variant report

Variant	rs239560
Chromosome Location	chr6:80722007-80722008
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10943681	0.91[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs10943682	0.92[ASN][1000 genomes]
rs10943688	0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1205578	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1205579	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs12526265	0.93[ASN][1000 genomes]
rs1410521	0.91[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1410522	0.91[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs151583	0.82[EUR][1000 genomes]
rs151587	0.81[EUR][1000 genomes]
rs151641	0.82[EUR][1000 genomes]
rs151642	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs151644	0.82[EUR][1000 genomes]
rs151645	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs151648	0.81[EUR][1000 genomes]
rs151654	0.82[EUR][1000 genomes]
rs151656	0.82[EUR][1000 genomes]
rs151657	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs151658	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs151660	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs151663	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs151664	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs151665	0.81[EUR][1000 genomes]
rs181177	0.81[EUR][1000 genomes]
rs1897870	0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1927425	0.86[CHB][hapmap]
rs1927426	0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs2181070	0.92[ASN][1000 genomes]
rs2295838	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2295840	0.93[ASN][1000 genomes]
rs2295841	0.91[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs239495	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs239496	0.83[EUR][1000 genomes]
rs239497	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs239500	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs239501	0.82[EUR][1000 genomes]
rs239502	0.82[EUR][1000 genomes]
rs239515	0.81[EUR][1000 genomes]
rs239552	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs239553	0.82[EUR][1000 genomes]
rs239554	0.85[CEU][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs239555	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs239558	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs239562	0.82[EUR][1000 genomes]
rs239563	0.82[EUR][1000 genomes]
rs239566	0.82[EUR][1000 genomes]
rs239567	0.82[EUR][1000 genomes]
rs239568	0.82[EUR][1000 genomes]
rs239569	0.81[EUR][1000 genomes]
rs239570	0.81[EUR][1000 genomes]
rs239571	0.81[EUR][1000 genomes]
rs239572	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs239573	0.83[EUR][1000 genomes]
rs239574	0.82[EUR][1000 genomes]
rs239577	0.81[EUR][1000 genomes]
rs239578	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs239579	0.81[EUR][1000 genomes]
rs239580	0.81[EUR][1000 genomes]
rs239581	0.80[EUR][1000 genomes]
rs239582	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs239583	0.93[JPT][hapmap]
rs239587	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs239589	0.85[CEU][hapmap]
rs240212	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs240213	0.88[CEU][hapmap];0.92[JPT][hapmap]
rs240214	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs240216	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs240217	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs240218	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs240225	0.82[EUR][1000 genomes]
rs240226	0.82[EUR][1000 genomes]
rs240228	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs240229	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs240237	0.82[EUR][1000 genomes]
rs2757084	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2769337	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3799497	0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs3812151	0.83[ASN][1000 genomes]
rs3828761	0.81[EUR][1000 genomes]
rs402128	0.82[EUR][1000 genomes]
rs465480	0.81[EUR][1000 genomes]
rs465483	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4706108	0.81[ASN][1000 genomes]
rs4706826	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4706827	0.91[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs587984	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61794	0.85[CEU][hapmap]
rs61795	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs61796	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs652752	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs653665	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs666040	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6923330	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6925415	0.86[ASN][1000 genomes]
rs9294168	0.92[ASN][1000 genomes]
rs9341801	0.91[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9341802	0.92[ASN][1000 genomes]
rs9341803	0.90[ASN][1000 genomes]
rs9343961	0.90[ASN][1000 genomes]
rs9343965	0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs9352790	0.92[ASN][1000 genomes]
rs9352797	0.83[ASN][1000 genomes]
rs9359406	0.90[ASN][1000 genomes]
rs9448877	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9448881	0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv5370	chr6:80715351-80751740	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs239560	ELOVL4	cis	Esophagus Muscularis	GTEx
rs239560	ELOVL4	cis	Artery Tibial	GTEx
rs239560	HTR1B	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80714800-80738800	Weak transcription	Small Intestine	intestine
2	chr6:80715000-80730400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:80715000-80748000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:80715000-80752200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:80715000-80752400	Weak transcription	Placenta	Placenta
6	chr6:80715200-80726000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:80715200-80727000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:80715200-80730800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:80715200-80734000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:80715200-80734400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:80715200-80739200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:80715200-80749600	Weak transcription	Fetal Intestine Small	intestine
13	chr6:80715200-80752000	Weak transcription	Primary B cells from cord blood	blood
14	chr6:80715200-80752200	Weak transcription	Primary T cells from cord blood	blood
15	chr6:80715400-80722600	Weak transcription	Fetal Intestine Large	intestine
16	chr6:80715400-80726000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:80715400-80727000	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:80715400-80729400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:80715400-80742200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:80715400-80743200	Weak transcription	Brain Germinal Matrix	brain
21	chr6:80715400-80745400	Weak transcription	Fetal Lung	lung
22	chr6:80715400-80755000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:80715400-80756800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:80715600-80724600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:80715600-80725200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:80715600-80739200	Weak transcription	Fetal Stomach	stomach
27	chr6:80715600-80754400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:80715600-80763800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr6:80715800-80733400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:80715800-80753600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:80715800-80753800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:80715800-80754400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:80716000-80723000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:80716000-80726000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:80716000-80728600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:80716000-80729400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:80716000-80739200	Weak transcription	NHEK	skin
38	chr6:80716000-80743600	Weak transcription	Fetal Heart	heart
39	chr6:80716200-80725200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:80716200-80727800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:80716200-80728000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:80716200-80754600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr6:80716400-80727800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:80716800-80753600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr6:80717000-80728000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:80717400-80722600	Strong transcription	HepG2	liver
47	chr6:80717400-80722800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr6:80717400-80724800	Strong transcription	NH-A	brain
49	chr6:80717400-80727400	Strong transcription	HUVEC	blood vessel
50	chr6:80717400-80728000	Strong transcription	H1 Cell Line	embryonic stem cell

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