Variant report

Variant	rs12600662
Chromosome Location	chr17:33894956-33894957
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	POLR2A	chr17:33894639-33895817	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:33894636-33895400	GM12878	blood:	n/a	n/a
3	YY1	chr17:33894553-33895306	GM12892	blood:	n/a	chr17:33894894-33894903 chr17:33894895-33894906 chr17:33895069-33895088
4	REST	chr17:33894734-33895337	PFSK-1	brain:	n/a	n/a
5	REST	chr17:33894451-33895556	HL-60	blood:	n/a	n/a
6	YY1	chr17:33894753-33895279	ECC-1	luminal epithelium:	n/a	chr17:33894894-33894903 chr17:33894895-33894906 chr17:33895069-33895088
7	POLR2A	chr17:33894635-33895766	GM12891	blood:	n/a	n/a
8	MAX	chr17:33894663-33895313	K562	blood:	n/a	chr17:33895064-33895073 chr17:33895065-33895076 chr17:33894892-33894902 chr17:33895066-33895075
9	RUNX3	chr17:33894597-33895340	GM12878	blood:	n/a	n/a
10	NFYA	chr17:33894835-33895341	K562	blood:	n/a	chr17:33895023-33895038 chr17:33895023-33895038 chr17:33895024-33895038 chr17:33895019-33895037
11	POLR2A	chr17:33894648-33895369	A549	lung:	n/a	n/a
12	POLR2A	chr17:33894729-33895027	SK-N-SH	brain:	n/a	n/a
13	MYC	chr17:33894663-33895920	K562	blood:	n/a	chr17:33895064-33895073 chr17:33895065-33895076 chr17:33894892-33894902 chr17:33895066-33895075
14	MYC	chr17:33894938-33895018	MCF-7	breast:	n/a	n/a
15	SIN3AK20	chr17:33894708-33895407	K562	blood:	n/a	n/a
16	CCNT2	chr17:33894758-33895341	K562	blood:	n/a	chr17:33894894-33894903
17	ZMIZ1	chr17:33894681-33895318	K562	blood:	n/a	n/a
18	TCF12	chr17:33894360-33895815	A549	lung:	n/a	chr17:33895157-33895167
19	POLR2A	chr17:33894453-33895437	HL-60	blood:	n/a	n/a
20	POLR2A	chr17:33894626-33895839	K562	blood:	n/a	n/a
21	POLR2A	chr17:33894676-33895861	HEK293	kidney:	n/a	n/a
22	USF1	chr17:33894788-33895296	SK-N-SH_RA	brain:	n/a	chr17:33895065-33895076
23	POLR2A	chr17:33894624-33895423	H1-neurons	neurons:	n/a	n/a
24	RFX5	chr17:33894779-33895277	HepG2	liver:	n/a	n/a
25	POLR2A	chr17:33894534-33895786	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr17:33894653-33895591	Raji	blood:	n/a	n/a
27	CREB1	chr17:33894626-33895421	GM12878	blood:	n/a	n/a
28	CHD2	chr17:33894708-33895421	Hela-S3	cervix:	n/a	n/a
29	TAF1	chr17:33894741-33895421	H1-neurons	neurons:	n/a	n/a
30	POLR2A	chr17:33894614-33895908	Hela-S3	cervix:	n/a	n/a
31	HEY1	chr17:33894622-33895765	K562	blood:	n/a	n/a
32	USF1	chr17:33894821-33895321	GM12878	blood:	n/a	chr17:33895065-33895076
33	TEAD4	chr17:33894611-33895010	K562	blood:	n/a	n/a
34	SRF	chr17:33894678-33895276	ECC-1	luminal epithelium:	n/a	chr17:33894892-33894902
35	TAF1	chr17:33894750-33895266	HepG2	liver:	n/a	n/a
36	CEBPD	chr17:33894753-33895210	HepG2	liver:	n/a	n/a
37	SRF	chr17:33894905-33895204	GM12878	blood:	n/a	n/a
38	ATF3	chr17:33894830-33895140	GM12878	blood:	n/a	chr17:33894894-33894903 chr17:33895066-33895086 chr17:33895005-33895018
39	POLR2A	chr17:33894546-33895688	GM12878	blood:	n/a	n/a
40	FOS	chr17:33894784-33895269	K562	blood:	n/a	n/a
41	NFIC	chr17:33894699-33895182	GM12878	blood:	n/a	n/a
42	BHLHE40	chr17:33894722-33895310	K562	blood:	n/a	n/a
43	POLR2A	chr17:33894724-33895386	H1-hESC	embryonic stem cell:	n/a	n/a
44	TBP	chr17:33894767-33895378	GM12878	blood:	n/a	n/a
45	ATF3	chr17:33894867-33895232	HepG2	liver:	n/a	chr17:33894894-33894903 chr17:33895066-33895086 chr17:33895005-33895018
46	NFYB	chr17:33894663-33895813	K562	blood:	n/a	chr17:33895023-33895038 chr17:33895025-33895040 chr17:33895023-33895038 chr17:33895024-33895038
47	POLR2A	chr17:33894627-33895315	GM12892	blood:	n/a	n/a
48	TAF1	chr17:33894736-33895274	GM12892	blood:	n/a	n/a
49	USF1	chr17:33894781-33895289	H1-hESC	embryonic stem cell:	n/a	chr17:33895065-33895076
50	E2F4	chr17:33894609-33895314	MCF10A-Er-Src	breast:	n/a	chr17:33894894-33894906 chr17:33895027-33895036 chr17:33894894-33894903

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:33894952-33895002	SK-N-SH_RA	brain:	n/a
2	chr17:33894952-33895002	PANC-1	pancreas:	n/a
3	chr17:33894952-33895002	HepG2	liver:	n/a
4	chr17:33894952-33895002	T-47D	breast:	n/a
5	chr17:33894952-33895002	HCT-116	colon:	n/a
6	chr17:33894952-33895002	AG04449	skin:	fetal
7	chr17:33894952-33895002	A549	lung:	n/a
8	chr17:33894952-33895002	U87	brain:	n/a
9	chr17:33894952-33895002	H1-hESC	embryonic stem cell:	embryo
10	chr17:33894952-33895002	PFSK-1	brain:	n/a
11	chr17:33894952-33895002	HMEC	breast:	n/a
12	chr17:33894952-33895002	AG09319	gingival:	n/a
13	chr17:33894952-33895002	NH-A	brain:	n/a
14	chr17:33894952-33895002	SAEC	small airway:	n/a
15	chr17:33894952-33895002	GM12891	blood:	n/a
16	chr17:33894952-33895002	HCF	heart:	n/a
17	chr17:33894952-33895002	NHDF-neo	bronchial:	n/a
18	chr17:33894952-33895002	ECC-1	luminal epithelium:	n/a
19	chr17:33894952-33895002	AG10803	skin:	n/a
20	chr17:33894952-33895002	GM06990	blood:	n/a
21	chr17:33894952-33895002	RPTEC	kidney:	n/a
22	chr17:33894952-33895002	LNCaP	prostate:	n/a
23	chr17:33894952-33895002	BE2_C	brain:	n/a
24	chr17:33894952-33895002	HCM	heart:	n/a
25	chr17:33894952-33895002	Hela-S3	cervix:	n/a
26	chr17:33894952-33895002	Jurkat	blood:	n/a
27	chr17:33894952-33895002	NT2-D1	testis:	n/a
28	chr17:33894952-33895002	IMR90	lung:	fetal
29	chr17:33894952-33895002	AG04450	lung:	fetal
30	chr17:33894952-33895002	NHBE	bronchial:	n/a
31	chr17:33894952-33895002	HRE	kidney:	n/a
32	chr17:33894952-33895002	HIPEpiC	eye:	n/a
33	chr17:33894952-33895002	MCF-7	breast:	n/a
34	chr17:33894952-33895002	HL-60	blood:	n/a
35	chr17:33894952-33895002	PrEC	prostate:	n/a
36	chr17:33894952-33895002	Hepatocyte	liver:	n/a
37	chr17:33894952-33895002	AoSMC	blood vessel:	n/a
38	chr17:33894952-33895002	AG09309	skin:	n/a
39	chr17:33894952-33895002	HNPCEpiC	eye:	n/a
40	chr17:33894952-33895002	MCF10A-Er-Src	breast:	n/a
41	chr17:33894952-33895002	SKMC	muscle:	n/a
42	chr17:33894952-33895002	GM19239	blood:	n/a
43	chr17:33894952-33895002	HEK293	kidney:	embryo
44	chr17:33894952-33895002	HRCEpiC	kidney:	n/a
45	chr17:33894952-33895002	HRPEpiC	eye:	n/a
46	chr17:33894952-33895002	SK-N-SH	brain:	n/a
47	chr17:33894952-33895002	SK-N-MC	brain:	n/a
48	chr17:33894952-33895002	HAEpiC	amniotic membrane:	n/a
49	chr17:33894952-33895002	GM12878	blood:	n/a
50	chr17:33894952-33895002	CMK	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:33893824..33895905-chr17:56735136..56737065,2	MCF-7	breast:
2	chr17:33891810..33896606-chr17:33903023..33907452,11	MCF-7	breast:
3	chr17:33893246..33896592-chr17:33904977..33907170,4	MCF-7	breast:
4	chr11:62323606..62324603-chr17:33894795..33895615,2	Hela-S3	cervix:
5	chr17:33893761..33897248-chr17:33899377..33902990,5	MCF-7	breast:
6	chr17:33891678..33894359-chr17:33894876..33897610,2	MCF-7	breast:
7	chr17:33894766..33896836-chr17:33913022..33916399,3	MCF-7	breast:
8	chr17:33886372..33890944-chr17:33891247..33895229,11	K562	blood:
9	chr1:154946171..154947021-chr17:33894708..33895221,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000267321	TF binding region
ENSG00000267321	CpG island
ENSG00000202077	Chromatin interaction
ENSG00000267625	Chromatin interaction
ENSG00000006125	Chromatin interaction
ENSG00000108733	Chromatin interaction
ENSG00000124942	Chromatin interaction
ENSG00000207297	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000242660	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1037591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10491114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs10491115	0.81[AMR][1000 genomes]
rs11870399	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12452633	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452961	0.81[ASN][1000 genomes]
rs12603142	0.82[AMR][1000 genomes]
rs16971117	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16971122	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1964509	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs226424	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs226427	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs226433	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs226435	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs226436	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2278950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2301731	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28384428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28384429	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28661650	0.81[AMR][1000 genomes]
rs3760325	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3785759	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62079728	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7211363	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9303689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9891317	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9904644	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs9904957	0.85[AMR][1000 genomes]
rs9906037	0.85[AMR][1000 genomes];0.81[ASN][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	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv960465	chr17:33891831-33894995	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33894000-33895400	Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr17:33894000-33895400	Active TSS	Fetal Lung	lung
3	chr17:33894000-33895800	Active TSS	Fetal Kidney	kidney
4	chr17:33894000-33896400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr17:33894000-33896400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr17:33894000-33896400	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr17:33894000-33897000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr17:33894200-33895200	Active TSS	Adipose Nuclei	Adipose
9	chr17:33894200-33895400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr17:33894200-33895400	Active TSS	Brain Hippocampus Middle	brain
11	chr17:33894200-33895400	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr17:33894200-33895400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr17:33894200-33895400	Active TSS	Rectal Smooth Muscle	rectum
14	chr17:33894200-33895600	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr17:33894200-33895600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr17:33894200-33895600	Active TSS	Brain Anterior Caudate	brain
17	chr17:33894200-33895800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr17:33894200-33896000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr17:33894200-33896200	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr17:33894200-33896200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:33894200-33896200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr17:33894200-33896200	Active TSS	Fetal Brain Female	brain
23	chr17:33894200-33896400	Active TSS	H1 Cell Line	embryonic stem cell
24	chr17:33894200-33896400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:33894200-33896400	Active TSS	Psoas Muscle	Psoas
26	chr17:33894200-33896600	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr17:33894200-33896600	Active TSS	A549	lung
28	chr17:33894200-33896600	Active TSS	K562	blood
29	chr17:33894200-33897000	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr17:33894400-33895000	Bivalent/Poised TSS	Fetal Stomach	stomach
31	chr17:33894400-33895200	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr17:33894400-33895200	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr17:33894400-33895200	Active TSS	Stomach Smooth Muscle	stomach
34	chr17:33894400-33895400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr17:33894400-33895400	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr17:33894400-33895400	Active TSS	Primary T cells from cord blood	blood
37	chr17:33894400-33895400	Active TSS	Brain Angular Gyrus	brain
38	chr17:33894400-33895400	Active TSS	Brain Germinal Matrix	brain
39	chr17:33894400-33895400	Active TSS	Colonic Mucosa	Colon
40	chr17:33894400-33895400	Active TSS	Duodenum Mucosa	Duodenum
41	chr17:33894400-33895400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr17:33894400-33895400	Active TSS	Fetal Intestine Small	intestine
43	chr17:33894400-33895400	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr17:33894400-33895400	Active TSS	Fetal Muscle Leg	muscle
45	chr17:33894400-33895400	Active TSS	Osteobl	bone
46	chr17:33894400-33895600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr17:33894400-33895600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr17:33894400-33895600	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr17:33894400-33895600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:33894400-33895600	Active TSS	Fetal Thymus	thymus

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