Variant report

Variant	rs6660202
Chromosome Location	chr1:67519422-67519423
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	chr1:67519337-67520220	MCF-7	breast:	n/a	n/a
2	POLR2A	chr1:67519306-67520275	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr1:67519292-67519768	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZBTB7A	chr1:67518972-67519568	K562	blood:	n/a	n/a
5	CEBPB	chr1:67518621-67520508	Hela-S3	cervix:	n/a	chr1:67519899-67519910 chr1:67519900-67519909
6	MAX	chr1:67518932-67520484	HCT-116	colon:	n/a	n/a
7	MYC	chr1:67519351-67519681	MCF10A-Er-Src	breast:	n/a	n/a
8	PML	chr1:67519347-67520348	K562	blood:	n/a	n/a
9	POLR2A	chr1:67519311-67520308	K562	blood:	n/a	n/a
10	CBX3	chr1:67519419-67520495	K562	blood:	n/a	n/a
11	CTCF	chr1:67519400-67519550	HCPEpiC	choroid plexus:	n/a	n/a
12	JUND	chr1:67519227-67519605	A549	lung:	n/a	chr1:67519357-67519366
13	RFX5	chr1:67519366-67520094	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:67519106-67520270	GM10847	blood:	n/a	n/a
15	POLR2A	chr1:67519232-67520226	HepG2	liver:	n/a	n/a
16	TBP	chr1:67518483-67520372	K562	blood:	n/a	n/a
17	TBL1XR1	chr1:67519335-67520146	K562	blood:	n/a	n/a
18	POLR2A	chr1:67519301-67520299	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr1:67518618-67520597	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr1:67518822-67520328	HL-60	blood:	n/a	n/a
21	POLR2A	chr1:67519060-67520354	ProgFib	skin:	n/a	n/a
22	CEBPD	chr1:67519418-67520347	K562	blood:	n/a	chr1:67519898-67519909
23	YY1	chr1:67519025-67520314	GM12878	blood:	n/a	chr1:67519832-67519841 chr1:67519326-67519340 chr1:67519717-67519731 chr1:67519720-67519729
24	GTF2B	chr1:67519389-67520465	K562	blood:	n/a	n/a
25	MTA3	chr1:67519336-67520472	GM12878	blood:	n/a	n/a
26	TCF7L2	chr1:67518750-67520281	Hela-S3	cervix:	n/a	n/a
27	YY1	chr1:67519289-67520283	ECC-1	luminal epithelium:	n/a	chr1:67519832-67519841 chr1:67519326-67519340 chr1:67519717-67519731 chr1:67519720-67519729
28	POLR2A	chr1:67518987-67520175	Hela-S3	cervix:	n/a	n/a
29	UBTF	chr1:67518470-67520391	K562	blood:	n/a	n/a
30	E2F6	chr1:67519283-67519475	K562	blood:	n/a	n/a
31	POLR2A	chr1:67519186-67520227	A549	lung:	n/a	n/a
32	ZNF263	chr1:67518529-67520421	HEK293-T-REx	kidney:	n/a	chr1:67520209-67520218
33	POLR2A	chr1:67518873-67520283	Hela-S3	cervix:	n/a	n/a
34	MAX	chr1:67519176-67520366	A549	lung:	n/a	n/a
35	REST	chr1:67519244-67520259	HL-60	blood:	n/a	chr1:67519372-67519382 chr1:67519335-67519348
36	ELF1	chr1:67519191-67520194	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:67519285-67520230	U87	brain:	n/a	n/a
38	POLR2A	chr1:67519112-67520380	H1-hESC	embryonic stem cell:	n/a	n/a
39	CREB1	chr1:67519129-67520165	A549	lung:	n/a	n/a
40	POLR2A	chr1:67519208-67520204	HepG2	liver:	n/a	n/a
41	POLR2A	chr1:67518927-67520292	GM12878	blood:	n/a	n/a
42	HNF4G	chr1:67519172-67520200	HepG2	liver:	n/a	chr1:67519407-67519421 chr1:67519415-67519423 chr1:67519413-67519421 chr1:67519407-67519422 chr1:67519409-67519421
43	RCOR1	chr1:67518506-67520325	K562	blood:	n/a	n/a
44	POLR2A	chr1:67519275-67520290	HCT-116	colon:	n/a	n/a
45	TFAP2C	chr1:67518491-67520380	Hela-S3	cervix:	n/a	n/a
46	MAX	chr1:67519406-67520378	NB4	blood:	n/a	n/a
47	POLR2A	chr1:67518571-67520348	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:67518967-67520304	NB4	blood:	n/a	n/a
49	TAF1	chr1:67519154-67520188	HepG2	liver:	n/a	n/a
50	MAX	chr1:67519102-67520399	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67519252..67520167-chr3:31573896..31574531,2	Hela-S3	cervix:

Variant related genes	Relation type
SLC35D1	TF binding region
ENSG00000163527	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11800236	0.95[EUR][1000 genomes]
rs11811977	0.95[EUR][1000 genomes]
rs55751500	0.95[EUR][1000 genomes]
rs56063179	0.95[EUR][1000 genomes]
rs58625335	0.95[EUR][1000 genomes]
rs60668571	0.95[EUR][1000 genomes]
rs72931926	0.95[EUR][1000 genomes]
rs72931930	0.95[EUR][1000 genomes]
rs72931938	0.95[EUR][1000 genomes]
rs74079200	0.95[EUR][1000 genomes]

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	nsv461751	chr1:67479598-67689036	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv546445	chr1:67479598-67689036	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	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	chr1:67516800-67520400	Active TSS	Fetal Intestine Large	intestine
2	chr1:67517400-67520800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:67517600-67519800	Active TSS	HMEC	breast
4	chr1:67517600-67520000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:67517600-67520200	Active TSS	K562	blood
6	chr1:67517600-67520400	Active TSS	Fetal Stomach	stomach
7	chr1:67517800-67519800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:67517800-67520000	Active TSS	Stomach Smooth Muscle	stomach
9	chr1:67517800-67520400	Active TSS	NHLF	lung
10	chr1:67517800-67520600	Active TSS	Right Atrium	heart
11	chr1:67517800-67520800	Active TSS	NH-A	brain
12	chr1:67518000-67519800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:67518000-67520200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr1:67518000-67520200	Active TSS	Placenta	Placenta
15	chr1:67518000-67520400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr1:67518000-67520400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:67518000-67520400	Active TSS	Aorta	Aorta
18	chr1:67518000-67520400	Active TSS	Ovary	ovary
19	chr1:67518000-67520400	Active TSS	Right Ventricle	heart
20	chr1:67518000-67520400	Active TSS	HSMM	muscle
21	chr1:67518000-67520600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:67518000-67520600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:67518000-67520600	Active TSS	Colonic Mucosa	Colon
24	chr1:67518000-67520600	Active TSS	Fetal Intestine Small	intestine
25	chr1:67518000-67520600	Active TSS	A549	lung
26	chr1:67518000-67520600	Active TSS	HSMMtube	muscle
27	chr1:67518200-67520200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:67518200-67520200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:67518200-67520200	Active TSS	Fetal Heart	heart
30	chr1:67518200-67520200	Active TSS	NHDF-Ad	bronchial
31	chr1:67518200-67520400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:67518200-67520400	Active TSS	Colon Smooth Muscle	Colon
33	chr1:67518200-67520400	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr1:67518200-67520600	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr1:67518200-67520600	Active TSS	Muscle Satellite Cultured Cells	--
36	chr1:67518200-67520600	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr1:67518200-67520600	Active TSS	GM12878-XiMat	blood
38	chr1:67518200-67520800	Active TSS	Fetal Kidney	kidney
39	chr1:67518400-67520200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:67518400-67520200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:67518400-67520200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:67518400-67520200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:67518400-67520200	Active TSS	Gastric	stomach
44	chr1:67518400-67520200	Active TSS	Small Intestine	intestine
45	chr1:67518400-67520200	Active TSS	Osteobl	bone
46	chr1:67518400-67520400	Active TSS	H1 Cell Line	embryonic stem cell
47	chr1:67518400-67520400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:67518400-67520400	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr1:67518400-67520400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:67518400-67520400	Active TSS	Brain Substantia Nigra	brain

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