Variant report

Variant	rs880062
Chromosome Location	chr6:35778989-35778990
allele	C/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	RFX5	chr6:35778781-35779305	Hela-S3	cervix:	n/a	n/a
2	GABPA	chr6:35778730-35779663	MCF-7	breast:	n/a	n/a
3	MAX	chr6:35778694-35779482	A549	lung:	n/a	n/a
4	RAD21	chr6:35778941-35779309	Hela-S3	cervix:	n/a	n/a
5	FOSL2	chr6:35778872-35779427	SK-N-SH	brain:	n/a	n/a
6	CEBPB	chr6:35778893-35779303	Hela-S3	cervix:	n/a	n/a
7	GABPA	chr6:35778620-35779624	A549	lung:	n/a	n/a
8	POLR2A	chr6:35778691-35779627	HCT-116	colon:	n/a	n/a
9	SP1	chr6:35778766-35779297	A549	lung:	n/a	n/a
10	JUND	chr6:35778884-35779340	Hela-S3	cervix:	n/a	chr6:35779167-35779178
11	GTF2F1	chr6:35778872-35779314	Hela-S3	cervix:	n/a	n/a
12	JUN	chr6:35778841-35779291	Hela-S3	cervix:	n/a	n/a
13	FOXA2	chr6:35778883-35779314	A549	lung:	n/a	n/a
14	GABPA	chr6:35778697-35779388	Hela-S3	cervix:	n/a	n/a
15	JUN	chr6:35778875-35779237	K562	blood:	n/a	n/a
16	POLR2A	chr6:35778755-35779408	HUVEC	blood vessel:	n/a	n/a
17	GATA3	chr6:35778705-35779431	A549	lung:	n/a	n/a
18	FOS	chr6:35778853-35779316	Hela-S3	cervix:	n/a	n/a
19	EP300	chr6:35778899-35779294	Hela-S3	cervix:	n/a	n/a
20	MAFK	chr6:35778982-35779250	HepG2	liver:	n/a	n/a
21	FOS	chr6:35778865-35779350	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr6:35778699-35779774	HCT-116	colon:	n/a	n/a
23	STAT3	chr6:35778802-35779678	MCF10A-Er-Src	breast:	n/a	chr6:35779644-35779651
24	STAT3	chr6:35778875-35779289	MCF10A-Er-Src	breast:	n/a	n/a
25	STAT3	chr6:35778863-35779374	MCF10A-Er-Src	breast:	n/a	n/a
26	FOSL2	chr6:35778893-35779243	A549	lung:	n/a	n/a
27	TBP	chr6:35778902-35779239	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr6:35778740-35779626	Hela-S3	cervix:	n/a	n/a
29	USF2	chr6:35778782-35779306	Hela-S3	cervix:	n/a	n/a
30	MAFK	chr6:35778953-35779290	IMR90	lung:	n/a	n/a
31	FOS	chr6:35778778-35779423	HUVEC	blood vessel:	n/a	n/a
32	TCF7L2	chr6:35778743-35780084	HCT-116	colon:	n/a	chr6:35779950-35779960 chr6:35779951-35779960 chr6:35779952-35779961 chr6:35779948-35779964 chr6:35779948-35779964 chr6:35779949-35779963
33	ELK1	chr6:35778875-35779333	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr6:35778694-35779617	HCT-116	colon:	n/a	n/a
35	TCF12	chr6:35778677-35779469	A549	lung:	n/a	n/a
36	USF1	chr6:35778861-35779108	A549	lung:	n/a	n/a
37	MAFK	chr6:35778840-35779304	Hela-S3	cervix:	n/a	n/a
38	MYC	chr6:35778808-35779202	MCF10A-Er-Src	breast:	n/a	n/a
39	MYC	chr6:35778887-35779252	MCF10A-Er-Src	breast:	n/a	n/a
40	MXI1	chr6:35778829-35779257	Hela-S3	cervix:	n/a	n/a
41	FOS	chr6:35778859-35779353	MCF10A-Er-Src	breast:	n/a	n/a
42	ELK4	chr6:35778788-35779276	Hela-S3	cervix:	n/a	n/a
43	ELF1	chr6:35778664-35779431	MCF-7	breast:	n/a	n/a
44	ZNF143	chr6:35778863-35779271	Hela-S3	cervix:	n/a	n/a
45	ELF1	chr6:35778690-35779379	K562	blood:	n/a	n/a
46	YY1	chr6:35778817-35779444	HCT-116	colon:	n/a	n/a
47	MAFF	chr6:35778982-35779209	HepG2	liver:	n/a	n/a
48	NR3C1	chr6:35778951-35779459	A549	lung:	n/a	chr6:35779286-35779299
49	NFYA	chr6:35778840-35779119	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr6:35778780-35779622	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
LHFPL5	TF binding region

Extended variants
information (count: 137 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10484264	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1049649	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10947572	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10947574	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10947576	0.87[ASN][1000 genomes]
rs11964319	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11968149	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1326752	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1326756	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17653835	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17654270	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17705020	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1887170	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2038962	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2051647	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2148533	0.81[EUR][1000 genomes]
rs2182546	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2250151	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2301510	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2395638	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2395640	0.81[EUR][1000 genomes]
rs2395641	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2395644	0.86[ASN][1000 genomes]
rs2395645	0.82[ASN][1000 genomes]
rs2395646	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2766519	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2766520	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2766521	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2766525	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2817022	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2817023	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2817027	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3891863	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3997732	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4340986	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs582526	0.84[EUR][1000 genomes]
rs59190698	0.81[EUR][1000 genomes]
rs595591	0.83[EUR][1000 genomes]
rs60467728	0.97[ASN][1000 genomes]
rs60696013	0.95[ASN][1000 genomes]
rs613540	0.82[EUR][1000 genomes]
rs640867	0.82[EUR][1000 genomes]
rs6457857	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457858	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457859	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457860	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6457862	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457864	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs657036	0.83[EUR][1000 genomes]
rs668438	0.82[EUR][1000 genomes]
rs671992	0.84[EUR][1000 genomes]
rs6905144	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6906455	0.91[ASN][1000 genomes]
rs6908433	0.84[ASN][1000 genomes]
rs6910260	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6910906	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6911849	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6916941	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6921531	0.82[ASN][1000 genomes]
rs6922695	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6923015	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6923312	0.83[EUR][1000 genomes]
rs6926156	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6931888	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6932973	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6933287	0.97[ASN][1000 genomes]
rs721694	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72919002	0.86[EUR][1000 genomes]
rs7740886	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7744924	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7749862	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7752545	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7752551	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755600	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7758042	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7763752	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7774060	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7776342	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs879668	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9296166	0.97[ASN][1000 genomes]
rs9462122	0.97[ASN][1000 genomes]
rs9462125	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9462127	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9462128	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9462131	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9462132	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9462133	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9462134	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9462135	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9462136	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9462141	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9462143	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9462144	0.83[ASN][1000 genomes]
rs9470111	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470118	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470119	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9470120	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470121	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470122	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470123	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9470124	0.95[ASN][1000 genomes]
rs9470125	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470126	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470130	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470131	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470136	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470138	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470139	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470140	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9470141	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9470142	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9470144	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9470147	0.81[EUR][1000 genomes]
rs9470151	0.95[ASN][1000 genomes]
rs9470152	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470153	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9470154	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9470155	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9470156	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9470157	0.87[ASN][1000 genomes]
rs9470161	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9470162	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9470166	0.84[ASN][1000 genomes]
rs9470167	0.84[ASN][1000 genomes]
rs9470169	0.84[ASN][1000 genomes]
rs9470172	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv821646	chr6:35604428-35802594	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv885802	chr6:35621781-35787417	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
6	nsv885803	chr6:35621781-35805133	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv885804	chr6:35621781-35809776	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv428143	chr6:35637083-35806504	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv885805	chr6:35685955-35779879	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	esv1791730	chr6:35754783-35805144	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv602939	chr6:35758072-35783497	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35773000-35791400	Weak transcription	Right Atrium	heart
2	chr6:35776200-35785000	Weak transcription	Brain Anterior Caudate	brain
3	chr6:35777000-35782400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:35777000-35801400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:35777800-35779800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr6:35778600-35779400	Enhancers	NH-A	brain
7	chr6:35778600-35779800	Flanking Active TSS	Hela-S3	cervix
8	chr6:35778600-35779800	Enhancers	HMEC	breast
9	chr6:35778600-35779800	Enhancers	HUVEC	blood vessel
10	chr6:35778600-35780200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:35778600-35780400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:35778800-35779000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:35778800-35779000	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr6:35778800-35779000	Enhancers	K562	blood
15	chr6:35778800-35779200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:35778800-35779200	Bivalent Enhancer	HepG2	liver
17	chr6:35778800-35779400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr6:35778800-35779400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr6:35778800-35779400	Enhancers	HSMM	muscle
20	chr6:35778800-35779600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:35778800-35779600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:35778800-35779600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:35778800-35779600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:35778800-35779600	Enhancers	Pancreas	Pancrea
25	chr6:35778800-35779600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr6:35778800-35779600	Flanking Active TSS	A549	lung
27	chr6:35778800-35779600	Enhancers	NHEK	skin
28	chr6:35778800-35779800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:35778800-35779800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:35778800-35779800	Enhancers	Osteobl	bone
31	chr6:35778800-35780400	Enhancers	Esophagus	oesophagus

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