Variant report

Variant	rs1705003
Chromosome Location	chr6:33385953-33385954
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	TAF1	chr6:33385473-33386570	K562	blood:	n/a	n/a
2	STAT3	chr6:33385863-33386427	MCF10A-Er-Src	breast:	n/a	chr6:33386222-33386231 chr6:33386221-33386230 chr6:33386220-33386231
3	POLR2A	chr6:33384094-33387006	PFSK-1	brain:	n/a	n/a
4	CEBPD	chr6:33385916-33386425	HepG2	liver:	n/a	n/a
5	MAX	chr6:33385642-33386460	HUVEC	blood vessel:	n/a	chr6:33386120-33386129 chr6:33385874-33385884 chr6:33385899-33385909 chr6:33386201-33386210 chr6:33386200-33386211
6	POLR2A	chr6:33385505-33386556	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:33385468-33386593	ECC-1	luminal epithelium:	n/a	n/a
8	USF1	chr6:33384939-33386624	K562	blood:	n/a	chr6:33386119-33386128 chr6:33386118-33386131 chr6:33386120-33386129 chr6:33386120-33386129
9	SIX5	chr6:33385847-33386351	GM12878	blood:	n/a	n/a
10	STAT1	chr6:33385395-33386566	Hela-S3	cervix:	n/a	chr6:33386220-33386231 chr6:33386222-33386231 chr6:33386221-33386230
11	USF1	chr6:33385509-33386589	ECC-1	luminal epithelium:	n/a	chr6:33386119-33386128 chr6:33386118-33386131 chr6:33386120-33386129 chr6:33386120-33386129
12	TAF1	chr6:33385562-33386522	K562	blood:	n/a	n/a
13	E2F6	chr6:33385267-33386415	K562	blood:	n/a	chr6:33386175-33386184
14	ZNF143	chr6:33385503-33386506	Hela-S3	cervix:	n/a	n/a
15	RUNX3	chr6:33385027-33387193	GM12878	blood:	n/a	n/a
16	TBL1XR1	chr6:33385646-33386494	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:33385471-33386497	MCF10A-Er-Src	breast:	n/a	n/a
18	MYBL2	chr6:33385458-33386538	HepG2	liver:	n/a	n/a
19	JUN	chr6:33384157-33388027	K562	blood:	n/a	chr6:33387272-33387283 chr6:33386177-33386186 chr6:33386981-33386990 chr6:33386847-33386856
20	TAF1	chr6:33385422-33386584	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr6:33385639-33386891	GM12892	blood:	n/a	n/a
22	BHLHE40	chr6:33385933-33386295	HepG2	liver:	n/a	chr6:33386119-33386128 chr6:33386118-33386131 chr6:33386120-33386129 chr6:33386120-33386129
23	MAX	chr6:33385239-33386682	HepG2	liver:	n/a	chr6:33386120-33386129 chr6:33385874-33385884 chr6:33385899-33385909 chr6:33386201-33386210 chr6:33386200-33386211
24	MAX	chr6:33385524-33386567	HepG2	liver:	n/a	chr6:33386120-33386129 chr6:33385874-33385884 chr6:33385899-33385909 chr6:33386201-33386210 chr6:33386200-33386211
25	MAX	chr6:33385545-33386560	K562	blood:	n/a	chr6:33386120-33386129 chr6:33385874-33385884 chr6:33385899-33385909 chr6:33386201-33386210 chr6:33386200-33386211
26	POLR2A	chr6:33385522-33386979	K562	blood:	n/a	n/a
27	POLR2A	chr6:33385502-33386594	HUVEC	blood vessel:	n/a	n/a
28	CEBPB	chr6:33385830-33386149	HepG2	liver:	n/a	n/a
29	USF1	chr6:33385408-33386688	HCT-116	colon:	n/a	chr6:33386119-33386128 chr6:33386118-33386131 chr6:33386120-33386129 chr6:33386120-33386129
30	POLR2A	chr6:33385451-33387100	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr6:33385530-33386445	H1-hESC	embryonic stem cell:	n/a	chr6:33386120-33386129 chr6:33385874-33385884 chr6:33385899-33385909 chr6:33386201-33386210 chr6:33386200-33386211
32	NFIC	chr6:33385584-33386409	GM12878	blood:	n/a	n/a
33	ZNF143	chr6:33385694-33386549	H1-hESC	embryonic stem cell:	n/a	n/a
34	SP1	chr6:33385710-33386393	K562	blood:	n/a	chr6:33386174-33386195
35	CUX1	chr6:33385847-33386276	GM12878	blood:	n/a	n/a
36	FOS	chr6:33385762-33386430	K562	blood:	n/a	chr6:33386177-33386186
37	CHD1	chr6:33385318-33386843	GM12878	blood:	n/a	n/a
38	ETS1	chr6:33385368-33386342	K562	blood:	n/a	n/a
39	ATF2	chr6:33385627-33386558	GM12878	blood:	n/a	n/a
40	HEY1	chr6:33385690-33387124	K562	blood:	n/a	chr6:33386980-33386989 chr6:33386982-33386991
41	HMGN3	chr6:33385650-33386390	K562	blood:	n/a	n/a
42	E2F4	chr6:33385499-33386496	K562	blood:	n/a	chr6:33386175-33386184
43	TCF7L2	chr6:33385550-33386439	PANC-1	pancreas:	n/a	n/a
44	ATF3	chr6:33385652-33386381	H1-hESC	embryonic stem cell:	n/a	chr6:33386120-33386140 chr6:33386109-33386129 chr6:33386120-33386129
45	POLR2A	chr6:33385702-33386022	GM12892	blood:	n/a	n/a
46	ZEB1	chr6:33385505-33386172	GM12878	blood:	n/a	n/a
47	THAP1	chr6:33385724-33386307	K562	blood:	n/a	n/a
48	TAF1	chr6:33384999-33386859	H1-neurons	neurons:	n/a	n/a
49	GTF2F1	chr6:33385805-33386257	H1-hESC	embryonic stem cell:	n/a	n/a
50	MXI1	chr6:33385532-33386354	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33385929-33385979	ECC-1	luminal epithelium:	n/a
2	chr6:33385929-33385979	HCT-116	colon:	n/a
3	chr6:33385929-33385979	HRE	kidney:	n/a
4	chr6:33385929-33385979	SKMC	muscle:	n/a
5	chr6:33385929-33385979	LNCaP	prostate:	n/a
6	chr6:33385929-33385979	MCF10A-Er-Src	breast:	n/a
7	chr6:33385929-33385979	NT2-D1	testis:	n/a
8	chr6:33385929-33385979	HPAEpiC	pulmonary alveolar:	n/a
9	chr6:33385929-33385979	Caco-2	colon:	n/a
10	chr6:33385929-33385979	NB4	blood:	n/a
11	chr6:33385929-33385979	PANC-1	pancreas:	n/a
12	chr6:33385929-33385979	GM12878	blood:	n/a
13	chr6:33385929-33385979	HUVEC	blood vessel:	n/a
14	chr6:33385929-33385979	GM12891	blood:	n/a
15	chr6:33385929-33385979	GM06990	blood:	n/a
16	chr6:33385929-33385979	AG09309	skin:	n/a
17	chr6:33385929-33385979	BJ	skin:	n/a
18	chr6:33385929-33385979	NHDF-neo	bronchial:	n/a
19	chr6:33385929-33385979	HCPEpiC	choroid plexus:	n/a
20	chr6:33385929-33385979	Hepatocyte	liver:	n/a
21	chr6:33385929-33385979	T-47D	breast:	n/a
22	chr6:33385929-33385979	PrEC	prostate:	n/a
23	chr6:33385929-33385979	HRCEpiC	kidney:	n/a
24	chr6:33385929-33385979	BE2_C	brain:	n/a
25	chr6:33385929-33385979	HEK293	kidney:	embryo
26	chr6:33385929-33385979	IMR90	lung:	fetal
27	chr6:33385929-33385979	PFSK-1	brain:	n/a
28	chr6:33385929-33385979	HIPEpiC	eye:	n/a
29	chr6:33385929-33385979	RPTEC	kidney:	n/a
30	chr6:33385929-33385979	ovcar-3	ovarian:	n/a
31	chr6:33385929-33385979	MCF-7	breast:	n/a
32	chr6:33385929-33385979	SK-N-MC	brain:	n/a
33	chr6:33385929-33385979	SAEC	small airway:	n/a
34	chr6:33385929-33385979	ProgFib	skin:	n/a
35	chr6:33385929-33385979	HAEpiC	amniotic membrane:	n/a
36	chr6:33385929-33385979	Hela-S3	cervix:	n/a
37	chr6:33385929-33385979	HL-60	blood:	n/a
38	chr6:33385929-33385979	AoSMC	blood vessel:	n/a
39	chr6:33385929-33385979	AG10803	skin:	n/a
40	chr6:33385929-33385979	HNPCEpiC	eye:	n/a
41	chr6:33385929-33385979	HRPEpiC	eye:	n/a
42	chr6:33385929-33385979	Jurkat	blood:	n/a
43	chr6:33385929-33385979	SK-N-SH_RA	brain:	n/a
44	chr6:33385929-33385979	HepG2	liver:	n/a
45	chr6:33385929-33385979	AG09319	gingival:	n/a
46	chr6:33385929-33385979	HCF	heart:	n/a
47	chr6:33385929-33385979	NHBE	bronchial:	n/a
48	chr6:33385929-33385979	CMK	blood:	n/a
49	chr6:33385929-33385979	GM12892	blood:	n/a
50	chr6:33385929-33385979	HMEC	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33279489..33293095-chr6:33375317..33398824,56	K562	blood:
2	chr6:33243299..33244923-chr6:33383429..33386295,2	MCF-7	breast:
3	chr6:32938527..32941573-chr6:33384163..33387216,4	K562	blood:
4	chr6:33385453..33389637-chr6:33419628..33424957,5	MCF-7	breast:
5	chr6:33264410..33268847-chr6:33383674..33387403,5	MCF-7	breast:
6	chr6:33168527..33171468-chr6:33384494..33387586,3	K562	blood:
7	chr6:33169269..33171468-chr6:33384494..33387192,2	K562	blood:
8	chr14:102828733..102829592-chr6:33385509..33386128,2	Hela-S3	cervix:
9	chr6:33254516..33257651-chr6:33384634..33387572,3	K562	blood:
10	chr6:33365854..33369434-chr6:33385468..33388336,3	K562	blood:
11	chr6:33255667..33257365-chr6:33384673..33386459,3	MCF-7	breast:
12	chr6:33264378..33268881-chr6:33383627..33388443,14	K562	blood:
13	chr6:33241747..33248128-chr6:33380775..33386072,13	K562	blood:
14	chr6:33383299..33386120-chr6:34202398..34204899,2	K562	blood:
15	chr6:33280795..33292485-chr6:33374786..33387605,31	K562	blood:
16	chr6:33356382..33361019-chr6:33384058..33388661,8	K562	blood:
17	chr6:33356706..33359588-chr6:33384249..33386179,3	MCF-7	breast:
18	chr6:33384548..33387250-chr6:33422114..33424496,2	K562	blood:
19	chr6:33285422..33287849-chr6:33385883..33388858,2	MCF-7	breast:
20	chr6:33264858..33266557-chr6:33385922..33387524,2	K562	blood:
21	chr6:33237639..33241732-chr6:33383253..33390116,11	K562	blood:
22	chr6:33239271..33241277-chr6:33383669..33386403,3	MCF-7	breast:
23	chr6:33357335..33362175-chr6:33383352..33389421,14	K562	blood:
24	chr6:33242542..33249529-chr6:33381747..33388277,18	K562	blood:
25	chr6:33358575..33362850-chr6:33383674..33386989,4	MCF-7	breast:
26	chr6:33371627..33375942-chr6:33381284..33387543,6	K562	blood:
27	chr6:33237802..33241730-chr6:33382199..33389112,10	K562	blood:
28	chr6:33255047..33257514-chr6:33384371..33386134,2	K562	blood:

Variant related genes	Relation type
SYNGAP1	TF binding region
CUTA	TF binding region
CUTA	CpG island
SYNGAP1	CpG island
ENSG00000236104	Chromatin interaction
ENSG00000204194	Chromatin interaction
ENSG00000196663	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000137309	Chromatin interaction
ENSG00000204220	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000225644	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000263756	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000112473	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000100865	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11757081	0.82[CHB][hapmap]
rs11759285	0.88[EUR][1000 genomes]
rs7752202	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9278004	0.82[EUR][1000 genomes]
rs9278039	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv885769	chr6:33377522-33412197	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv602832	chr6:33382241-33520221	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv932196	chr6:33383131-33400706	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1705003	UHRF1BP1	cis	cerebellum	SCAN
rs1705003	HLA-DQA1	cis	lymphoblastoid	seeQTL
rs1705003	HLA-DRB5	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33384000-33386600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:33384400-33386000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr6:33384400-33386400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:33384400-33386600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:33384600-33386200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:33384600-33386200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:33384600-33386200	Active TSS	NHLF	lung
8	chr6:33384600-33386400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr6:33384600-33386400	Active TSS	Lung	lung
10	chr6:33384600-33386800	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr6:33384800-33386000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:33384800-33386200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:33384800-33386200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:33384800-33386200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr6:33384800-33386200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:33384800-33386200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:33384800-33386200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:33384800-33386200	Active TSS	GM12878-XiMat	blood
19	chr6:33384800-33386200	Active TSS	HSMM	muscle
20	chr6:33384800-33386200	Active TSS	NH-A	brain
21	chr6:33384800-33386400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr6:33384800-33386400	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr6:33384800-33386400	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr6:33384800-33386400	Active TSS	Fetal Kidney	kidney
25	chr6:33384800-33386400	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr6:33384800-33386400	Active TSS	A549	lung
27	chr6:33384800-33386600	Active TSS	Ovary	ovary
28	chr6:33384800-33386600	Active TSS	Psoas Muscle	Psoas
29	chr6:33384800-33386800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr6:33385000-33386000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:33385000-33386200	Active TSS	H1 Cell Line	embryonic stem cell
32	chr6:33385000-33386200	Active TSS	Muscle Satellite Cultured Cells	--
33	chr6:33385000-33386200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:33385000-33386200	Active TSS	Colonic Mucosa	Colon
35	chr6:33385000-33386200	Active TSS	Fetal Intestine Large	intestine
36	chr6:33385000-33386200	Active TSS	Osteobl	bone
37	chr6:33385000-33386400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:33385000-33386400	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr6:33385000-33386400	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr6:33385000-33386400	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr6:33385000-33386400	Active TSS	Aorta	Aorta
42	chr6:33385000-33386400	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr6:33385000-33386600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:33385000-33386600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:33385000-33387000	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr6:33385200-33386000	Active TSS	Gastric	stomach
47	chr6:33385200-33386200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:33385200-33386200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:33385200-33386200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:33385200-33386200	Active TSS	Primary T helper naive cells from peripheral blood	blood

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