Variant report

Variant	rs3818532
Chromosome Location	chr6:33679807-33679808
allele	A/G
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	REST	chr6:33678408-33680143	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr6:33678953-33679883	GM12878	blood:	n/a	n/a
3	KAP1	chr6:33679117-33679996	HEK293	kidney:	n/a	n/a
4	POLR2A	chr6:33678664-33679863	GM19193	blood:	n/a	n/a
5	MAX	chr6:33679015-33679911	HepG2	liver:	n/a	chr6:33679273-33679283 chr6:33679204-33679215
6	NRF1	chr6:33678907-33680092	SK-N-SH	brain:	n/a	chr6:33679231-33679240 chr6:33679517-33679526 chr6:33679515-33679529 chr6:33679231-33679245 chr6:33679571-33679582 chr6:33679515-33679526 chr6:33679233-33679242 chr6:33679231-33679242 chr6:33679228-33679242 chr6:33679568-33679582 chr6:33679231-33679242
7	E2F4	chr6:33679065-33679863	MCF10A-Er-Src	breast:	n/a	chr6:33679222-33679236 chr6:33679476-33679487 chr6:33679516-33679525 chr6:33679232-33679241 chr6:33679487-33679498
8	POLR2A	chr6:33678990-33679902	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr6:33679066-33679853	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:33679031-33679960	GM18526	blood:	n/a	n/a
11	ARID3A	chr6:33679294-33679869	HepG2	liver:	n/a	n/a
12	POLR2A	chr6:33679224-33679851	GM12891	blood:	n/a	n/a
13	MAX	chr6:33678924-33679935	HepG2	liver:	n/a	chr6:33679273-33679283 chr6:33679204-33679215
14	POLR2A	chr6:33678971-33679823	HCT-116	colon:	n/a	n/a
15	RELA	chr6:33679061-33679982	GM15510	blood:	n/a	n/a
16	TAF1	chr6:33679060-33679860	H1-neurons	neurons:	n/a	n/a
17	MAX	chr6:33678826-33679862	MCF-7	breast:	n/a	chr6:33679273-33679283 chr6:33679204-33679215
18	TAF1	chr6:33678882-33679938	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr6:33679009-33679848	GM12892	blood:	n/a	n/a
20	POLR2A	chr6:33678151-33680011	GM12891	blood:	n/a	n/a
21	RCOR1	chr6:33679266-33679873	HepG2	liver:	n/a	n/a
22	CTCF	chr6:33678674-33680111	SK-N-SH	brain:	n/a	n/a
23	RAD21	chr6:33679300-33679960	A549	lung:	n/a	n/a
24	EP300	chr6:33679626-33680058	GM12878	blood:	n/a	n/a
25	MAX	chr6:33678955-33680000	GM12878	blood:	n/a	chr6:33679273-33679283 chr6:33679204-33679215
26	PML	chr6:33678348-33679985	GM12878	blood:	n/a	n/a
27	SIN3A	chr6:33679110-33679943	H1-hESC	embryonic stem cell:	n/a	n/a
28	NRF1	chr6:33679038-33679951	GM12878	blood:	n/a	chr6:33679231-33679240 chr6:33679517-33679526 chr6:33679515-33679529 chr6:33679231-33679245 chr6:33679571-33679582 chr6:33679515-33679526 chr6:33679233-33679242 chr6:33679231-33679242 chr6:33679228-33679242 chr6:33679568-33679582 chr6:33679231-33679242
29	CEBPB	chr6:33679276-33679824	Hela-S3	cervix:	n/a	n/a
30	EBF1	chr6:33679581-33679933	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:33679037-33679856	H1-neurons	neurons:	n/a	n/a
32	POU2F2	chr6:33679598-33679922	GM12878	blood:	n/a	chr6:33679806-33679816 chr6:33679789-33679797 chr6:33679806-33679815 chr6:33679800-33679822 chr6:33679788-33679797 chr6:33679807-33679814 chr6:33679803-33679818 chr6:33679787-33679797 chr6:33679787-33679797
33	FOXM1	chr6:33678961-33679978	GM12878	blood:	n/a	n/a
34	MAX	chr6:33678814-33679849	H1-hESC	embryonic stem cell:	n/a	chr6:33679273-33679283 chr6:33679204-33679215
35	UBTF	chr6:33679180-33679837	K562	blood:	n/a	n/a
36	POLR2A	chr6:33678756-33679895	GM18505	blood:	n/a	n/a
37	SMC3	chr6:33679282-33679994	GM12878	blood:	n/a	n/a
38	RUNX3	chr6:33678969-33680057	GM12878	blood:	n/a	n/a
39	MYC	chr6:33678729-33679813	K562	blood:	n/a	chr6:33679273-33679283 chr6:33679204-33679215
40	EP300	chr6:33679228-33679944	GM12878	blood:	n/a	n/a
41	POLR2A	chr6:33678274-33680020	Raji	blood:	n/a	n/a
42	POLR2A	chr6:33678927-33679878	SK-N-MC	brain:	n/a	n/a
43	CTCF	chr6:33679314-33680092	A549	lung:	n/a	n/a
44	POLR2A	chr6:33678488-33679808	K562	blood:	n/a	n/a
45	POLR2A	chr6:33678004-33679877	HepG2	liver:	n/a	n/a
46	IRF1	chr6:33679098-33679808	K562	blood:	n/a	chr6:33679265-33679279
47	POLR2A	chr6:33679014-33679998	GM18951	blood:	n/a	n/a
48	MTA3	chr6:33678510-33680065	GM12878	blood:	n/a	n/a
49	CTCF	chr6:33679398-33679926	GM12878	blood:	n/a	n/a
50	MYC	chr6:33678645-33679823	K562	blood:	n/a	chr6:33679273-33679283 chr6:33679204-33679215

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33679775-33679825	HRPEpiC	eye:	n/a
2	chr6:33679775-33679825	LNCaP	prostate:	n/a
3	chr6:33679775-33679825	HRE	kidney:	n/a
4	chr6:33679775-33679825	SK-N-MC	brain:	n/a
5	chr6:33679775-33679825	PrEC	prostate:	n/a
6	chr6:33679775-33679825	NHDF-neo	bronchial:	n/a
7	chr6:33679775-33679825	GM06990	blood:	n/a
8	chr6:33679775-33679825	SK-N-SH	brain:	n/a
9	chr6:33679775-33679825	HAEpiC	amniotic membrane:	n/a
10	chr6:33679775-33679825	K562	blood:	n/a
11	chr6:33679775-33679825	BJ	skin:	n/a
12	chr6:33679775-33679825	NHBE	bronchial:	n/a
13	chr6:33679775-33679825	CMK	blood:	n/a
14	chr6:33679775-33679825	GM12878	blood:	n/a
15	chr6:33679775-33679825	HL-60	blood:	n/a
16	chr6:33679775-33679825	HEK293	kidney:	embryo
17	chr6:33679775-33679825	AG04450	lung:	fetal
18	chr6:33679775-33679825	AG09309	skin:	n/a
19	chr6:33679775-33679825	SK-N-SH_RA	brain:	n/a
20	chr6:33679775-33679825	Hela-S3	cervix:	n/a
21	chr6:33679775-33679825	MCF-7	breast:	n/a
22	chr6:33679775-33679825	AG09319	gingival:	n/a
23	chr6:33679775-33679825	GM12891	blood:	n/a
24	chr6:33679775-33679825	Hepatocyte	liver:	n/a
25	chr6:33679775-33679825	ovcar-3	ovarian:	n/a
26	chr6:33679775-33679825	HCF	heart:	n/a
27	chr6:33679775-33679825	HNPCEpiC	eye:	n/a
28	chr6:33679775-33679825	AG04449	skin:	fetal
29	chr6:33679775-33679825	HCT-116	colon:	n/a
30	chr6:33679775-33679825	HepG2	liver:	n/a
31	chr6:33679775-33679825	ECC-1	luminal epithelium:	n/a
32	chr6:33679775-33679825	PANC-1	pancreas:	n/a
33	chr6:33679775-33679825	SAEC	small airway:	n/a
34	chr6:33679775-33679825	NB4	blood:	n/a
35	chr6:33679775-33679825	AoSMC	blood vessel:	n/a
36	chr6:33679775-33679825	ProgFib	skin:	n/a
37	chr6:33679775-33679825	Caco-2	colon:	n/a
38	chr6:33679775-33679825	GM19239	blood:	n/a
39	chr6:33679775-33679825	NT2-D1	testis:	n/a
40	chr6:33679775-33679825	RPTEC	kidney:	n/a
41	chr6:33679775-33679825	Jurkat	blood:	n/a
42	chr6:33679775-33679825	AG10803	skin:	n/a
43	chr6:33679775-33679825	NH-A	brain:	n/a
44	chr6:33679775-33679825	HUVEC	blood vessel:	n/a
45	chr6:33679775-33679825	HRCEpiC	kidney:	n/a
46	chr6:33679775-33679825	HIPEpiC	eye:	n/a
47	chr6:33679775-33679825	GM12892	blood:	n/a
48	chr6:33679775-33679825	H1-hESC	embryonic stem cell:	embryo
49	chr6:33679775-33679825	HEEpiC	esophagus:	n/a
50	chr6:33679775-33679825	T-47D	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33265365..33267205-chr6:33677898..33679962,2	K562	blood:
2	chr6:33677651..33679939-chr6:34111673..34114600,2	MCF-7	breast:
3	chr6:33679645..33680333-chr6:34022737..34023251,2	K562	blood:
4	chr6:33264498..33266775-chr6:33678035..33680124,2	MCF-7	breast:
5	chr6:33588748..33590902-chr6:33677628..33680104,3	K562	blood:
6	chr6:33588748..33590595-chr6:33677611..33680104,2	K562	blood:
7	chr6:33678240..33679964-chr6:34113479..34115343,2	MCF-7	breast:
8	chr6:33679525..33680115-chr6:34122329..34123229,3	MCF-7	breast:
9	chr6:33587667..33592228-chr6:33677016..33679936,5	MCF-7	breast:
10	chr6:33555432..33562879-chr6:33670455..33680174,12	K562	blood:
11	chr6:33677771..33685795-chr6:33753004..33758704,10	MCF-7	breast:
12	chr6:33660515..33666072-chr6:33673200..33680629,8	MCF-7	breast:
13	chr6:33677680..33679812-chr6:33755384..33758328,2	MCF-7	breast:
14	chr6:33678014..33680671-chr6:33755515..33757218,2	K562	blood:

Variant related genes	Relation type
UQCC2	TF binding region
UQCC2	CpG island
ENSG00000269490	Chromatin interaction
ENSG00000096433	Chromatin interaction
ENSG00000266509	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000197251	Chromatin interaction
ENSG00000124493	Chromatin interaction
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10456075	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10456420	1.00[ASN][1000 genomes]
rs10456421	1.00[ASN][1000 genomes]
rs10947415	0.84[CEU][hapmap]
rs10947426	0.87[AFR][1000 genomes]
rs10947432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10947441	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap]
rs10947442	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11755817	1.00[JPT][hapmap]
rs11757379	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs12153870	0.87[AFR][1000 genomes]
rs12153877	1.00[ASN][1000 genomes]
rs12189725	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs12190155	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs12192087	1.00[ASN][1000 genomes]
rs12193658	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195409	1.00[ASN][1000 genomes]
rs12195707	0.84[CEU][hapmap];0.87[AFR][1000 genomes]
rs12198383	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12199132	0.81[EUR][1000 genomes]
rs12203688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12204620	1.00[ASN][1000 genomes]
rs12204992	1.00[ASN][1000 genomes]
rs12205398	0.94[EUR][1000 genomes]
rs12205667	0.87[AFR][1000 genomes]
rs12211490	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap]
rs12214669	1.00[LWK][hapmap]
rs12661400	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12662447	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203745	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap]
rs13204162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs13204975	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13214874	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13220421	0.87[AFR][1000 genomes]
rs2274459	1.00[ASW][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap]
rs2281831	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2281917	0.85[CEU][hapmap];0.96[EUR][1000 genomes]
rs2281918	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2281919	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2296340	1.00[JPT][hapmap]
rs2296737	0.96[EUR][1000 genomes]
rs34460651	0.92[ASN][1000 genomes]
rs34517899	0.87[AFR][1000 genomes]
rs34778247	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35088242	0.87[AFR][1000 genomes]
rs35095444	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35445446	1.00[ASN][1000 genomes]
rs35698850	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs35964955	0.92[ASN][1000 genomes]
rs36097803	0.87[AFR][1000 genomes]
rs3748080	1.00[JPT][hapmap]
rs3793080	0.80[TSI][hapmap]
rs3806107	0.80[TSI][hapmap]
rs3818526	0.97[EUR][1000 genomes]
rs435945	1.00[JPT][hapmap]
rs4559081	1.00[LWK][hapmap]
rs66617522	1.00[ASN][1000 genomes]
rs72880510	0.91[ASN][1000 genomes]
rs729376	0.81[EUR][1000 genomes]
rs877187	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs9296097	0.92[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs9469554	0.92[CEU][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.88[EUR][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	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3818532	C6orf125	cis	cerebellum	SCAN
rs3818532	ITPR3	cis	multi-tissue	Pritchard
rs3818532	LEMD2	cis	cerebellum	SCAN
rs3818532	LEMD2	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33678600-33680000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr6:33678600-33680000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr6:33678600-33680200	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr6:33678800-33680000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:33678800-33680000	Active TSS	Aorta	Aorta
6	chr6:33678800-33680000	Active TSS	Esophagus	oesophagus
7	chr6:33678800-33680000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr6:33679000-33680000	Active TSS	Brain Angular Gyrus	brain
9	chr6:33679000-33680000	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr6:33679000-33680000	Active TSS	Psoas Muscle	Psoas
11	chr6:33679000-33680200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:33679200-33680000	Active TSS	Colonic Mucosa	Colon
13	chr6:33679200-33680000	Active TSS	Fetal Muscle Trunk	muscle
14	chr6:33679200-33680200	Enhancers	Fetal Heart	heart
15	chr6:33679600-33680000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:33679600-33680000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:33679600-33680000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr6:33679600-33680000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:33679600-33680000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr6:33679600-33680000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:33679600-33680000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr6:33679600-33680000	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr6:33679600-33680000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr6:33679600-33680000	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr6:33679600-33680000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr6:33679600-33680000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr6:33679600-33680000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr6:33679600-33680000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr6:33679600-33680000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr6:33679600-33680000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:33679600-33680000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr6:33679600-33680000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr6:33679600-33680000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:33679600-33680000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:33679600-33680000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:33679600-33680000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr6:33679600-33680000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:33679600-33680000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:33679600-33680000	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr6:33679600-33680000	Flanking Active TSS	Liver	Liver
41	chr6:33679600-33680000	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr6:33679600-33680000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr6:33679600-33680000	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr6:33679600-33680000	Flanking Active TSS	Fetal Intestine Large	intestine
45	chr6:33679600-33680000	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr6:33679600-33680000	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr6:33679600-33680000	Flanking Active TSS	Fetal Stomach	stomach
48	chr6:33679600-33680000	Flanking Active TSS	Fetal Thymus	thymus
49	chr6:33679600-33680000	Enhancers	Placenta Amnion	Placenta Amnion
50	chr6:33679600-33680000	Enhancers	Sigmoid Colon	Sigmoid Colon

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