Variant report

Variant	rs12066551
Chromosome Location	chr1:169863657-169863658
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	JUND	chr1:169862593-169863706	A549	lung:	n/a	chr1:169863455-169863464 chr1:169863477-169863486
2	POLR2A	chr1:169861889-169863963	GM19099	blood:	n/a	n/a
3	ELF1	chr1:169862511-169863663	K562	blood:	n/a	n/a
4	RFX5	chr1:169861477-169864046	SK-N-SH	brain:	n/a	chr1:169863478-169863487
5	SP2	chr1:169862721-169863692	HepG2	liver:	n/a	n/a
6	CHD2	chr1:169862421-169863766	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:169862452-169863851	MCF-7	breast:	n/a	n/a
8	TAF1	chr1:169863433-169863734	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr1:169862149-169864267	H1-hESC	embryonic stem cell:	n/a	n/a
10	ATF2	chr1:169862830-169863705	GM12878	blood:	n/a	chr1:169863454-169863465
11	MAX	chr1:169862446-169863753	K562	blood:	n/a	n/a
12	TCF7L2	chr1:169862958-169863691	Hela-S3	cervix:	n/a	n/a
13	E2F6	chr1:169862987-169863913	A549	lung:	n/a	chr1:169863454-169863463 chr1:169863479-169863488 chr1:169863350-169863365 chr1:169863456-169863465
14	POLR2A	chr1:169862354-169864005	ProgFib	skin:	n/a	n/a
15	NFYB	chr1:169862967-169863706	GM12878	blood:	n/a	chr1:169863475-169863490 chr1:169863475-169863490 chr1:169863479-169863491 chr1:169863127-169863137 chr1:169863477-169863492 chr1:169863476-169863490
16	SP1	chr1:169862792-169863730	A549	lung:	n/a	chr1:169863468-169863489
17	TAL1	chr1:169862648-169864025	K562	blood:	n/a	n/a
18	CREB1	chr1:169862356-169863786	HepG2	liver:	n/a	chr1:169863453-169863466
19	POLR2A	chr1:169862470-169864082	SK-N-SH	brain:	n/a	n/a
20	HCFC1	chr1:169861435-169864287	Hela-S3	cervix:	n/a	n/a
21	SMARCB1	chr1:169862319-169863947	Hela-S3	cervix:	n/a	n/a
22	FOS	chr1:169863001-169863732	MCF10A-Er-Src	breast:	n/a	chr1:169863455-169863464 chr1:169863477-169863486
23	POLR2A	chr1:169862495-169864014	HEK293	kidney:	n/a	n/a
24	CREB1	chr1:169862480-169863800	GM12878	blood:	n/a	chr1:169863453-169863466
25	MAZ	chr1:169862544-169863819	GM12878	blood:	n/a	n/a
26	CREB1	chr1:169862518-169863961	K562	blood:	n/a	chr1:169863453-169863466
27	POLR2A	chr1:169862376-169863791	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr1:169861160-169864335	GM12878	blood:	n/a	n/a
29	ELK1	chr1:169862654-169863892	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr1:169862090-169863924	Hela-S3	cervix:	n/a	n/a
31	STAT3	chr1:169862941-169863898	MCF10A-Er-Src	breast:	n/a	chr1:169863112-169863120
32	MAX	chr1:169862897-169863781	SK-N-SH	brain:	n/a	n/a
33	TBL1XR1	chr1:169862844-169863897	K562	blood:	n/a	n/a
34	POLR2A	chr1:169862539-169863801	MCF-7	breast:	n/a	n/a
35	TBP	chr1:169862119-169863861	K562	blood:	n/a	n/a
36	KAP1	chr1:169862947-169863844	HEK293	kidney:	n/a	n/a
37	TAF1	chr1:169862441-169863684	GM12878	blood:	n/a	n/a
38	ELF1	chr1:169862573-169863883	HCT-116	colon:	n/a	n/a
39	ZNF143	chr1:169862877-169863657	H1-hESC	embryonic stem cell:	n/a	n/a
40	ZNF143	chr1:169862853-169863677	K562	blood:	n/a	n/a
41	YY1	chr1:169862547-169863697	A549	lung:	n/a	chr1:169863368-169863376 chr1:169862643-169862654 chr1:169863190-169863212 chr1:169863357-169863379 chr1:169863369-169863379 chr1:169863189-169863201
42	POLR2A	chr1:169863338-169863770	U87	brain:	n/a	n/a
43	POLR2A	chr1:169862505-169863878	PFSK-1	brain:	n/a	n/a
44	MYC	chr1:169862755-169863752	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr1:169861987-169864125	K562	blood:	n/a	n/a
46	CUX1	chr1:169862987-169863717	K562	blood:	n/a	n/a
47	CREB1	chr1:169862859-169863711	ECC-1	luminal epithelium:	n/a	chr1:169863453-169863466
48	YY1	chr1:169862337-169863686	HepG2	liver:	n/a	chr1:169863368-169863376 chr1:169862643-169862654 chr1:169863190-169863212 chr1:169863357-169863379 chr1:169863369-169863379 chr1:169863189-169863201
49	GATA3	chr1:169863301-169863993	T-47D	breast:	n/a	n/a
50	ELF1	chr1:169862816-169863702	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169861326..169864449-chr1:170043806..170046469,4	K562	blood:
2	chr1:169863583..169866323-chr1:169872602..169875354,3	MCF-7	breast:
3	chr1:169862596..169865250-chr1:170499667..170504019,5	K562	blood:
4	chr1:169862763..169864506-chr1:170500944..170502450,2	K562	blood:
5	chr1:169862177..169865166-chr1:170500254..170502788,2	MCF-7	breast:
6	chr1:169863487..169865405-chr1:169882715..169884373,2	K562	blood:
7	chr1:169763753..169765531-chr1:169862183..169864517,2	MCF-7	breast:
8	chr1:169763994..169765974-chr1:169862962..169865288,2	K562	blood:
9	chr1:169862471..169864194-chr12:53738889..53741815,2	MCF-7	breast:

Variant related genes	Relation type
SCYL3	TF binding region
ENSG00000171806	Chromatin interaction
ENSG00000120370	Chromatin interaction
ENSG00000000460	Chromatin interaction
ENSG00000170374	Chromatin interaction
ENSG00000075945	Chromatin interaction
ENSG00000231407	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10458398	1.00[ASN][1000 genomes]
rs10800487	1.00[ASN][1000 genomes]
rs10919267	0.84[ASN][1000 genomes]
rs10919268	1.00[ASN][1000 genomes]
rs10919269	1.00[ASN][1000 genomes]
rs10919276	1.00[EUR][1000 genomes]
rs10919288	1.00[EUR][1000 genomes]
rs10919294	1.00[EUR][1000 genomes]
rs10919295	1.00[EUR][1000 genomes]
rs10919296	1.00[EUR][1000 genomes]
rs10919300	1.00[EUR][1000 genomes]
rs12023729	1.00[ASN][1000 genomes]
rs12024570	1.00[ASN][1000 genomes]
rs12025296	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027790	1.00[ASN][1000 genomes]
rs12035711	1.00[ASN][1000 genomes]
rs12044536	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12071325	1.00[EUR][1000 genomes]
rs12076018	1.00[EUR][1000 genomes]
rs12077708	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079608	1.00[EUR][1000 genomes]
rs12083317	1.00[ASN][1000 genomes]
rs12090220	1.00[EUR][1000 genomes]
rs12095784	1.00[EUR][1000 genomes]
rs13374781	1.00[EUR][1000 genomes]
rs13375701	1.00[EUR][1000 genomes]
rs16862886	1.00[EUR][1000 genomes]
rs16862978	1.00[EUR][1000 genomes]
rs2103641	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272912	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272915	1.00[ASN][1000 genomes]
rs2901261	1.00[EUR][1000 genomes]
rs4279900	1.00[EUR][1000 genomes]
rs56084868	1.00[EUR][1000 genomes]
rs57038529	1.00[EUR][1000 genomes]
rs73041439	1.00[EUR][1000 genomes]
rs74121797	1.00[EUR][1000 genomes]
rs74122312	1.00[EUR][1000 genomes]
rs74122421	1.00[EUR][1000 genomes]
rs74122422	1.00[EUR][1000 genomes]
rs74122452	1.00[EUR][1000 genomes]
rs7531947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532990	1.00[ASN][1000 genomes]
rs7533350	1.00[ASN][1000 genomes]
rs989054	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169861200-169863800	Active TSS	Aorta	Aorta
2	chr1:169861200-169864000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr1:169861400-169864000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:169861400-169864000	Active TSS	Colonic Mucosa	Colon
5	chr1:169861600-169863800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:169861600-169863800	Active TSS	H1 Cell Line	embryonic stem cell
7	chr1:169861600-169863800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:169861600-169863800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:169861600-169863800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:169861600-169863800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:169861600-169863800	Active TSS	GM12878-XiMat	blood
12	chr1:169861600-169863800	Active TSS	HSMM	muscle
13	chr1:169861600-169864000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:169861600-169864000	Active TSS	Psoas Muscle	Psoas
15	chr1:169861600-169864000	Active TSS	Right Atrium	heart
16	chr1:169861600-169864000	Active TSS	HSMMtube	muscle
17	chr1:169861800-169863800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:169861800-169863800	Active TSS	Fetal Muscle Trunk	muscle
19	chr1:169861800-169863800	Active TSS	Stomach Mucosa	stomach
20	chr1:169861800-169863800	Active TSS	NHDF-Ad	bronchial
21	chr1:169861800-169864000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr1:169861800-169864000	Active TSS	Esophagus	oesophagus
23	chr1:169861800-169864000	Active TSS	Left Ventricle	heart
24	chr1:169861800-169864000	Active TSS	Placenta Amnion	Placenta Amnion
25	chr1:169861800-169864000	Active TSS	Right Ventricle	heart
26	chr1:169862000-169863800	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr1:169862000-169863800	Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr1:169862000-169863800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:169862000-169863800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:169862000-169863800	Active TSS	Liver	Liver
31	chr1:169862000-169863800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:169862000-169863800	Active TSS	Brain Substantia Nigra	brain
33	chr1:169862000-169863800	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr1:169862000-169863800	Active TSS	Fetal Intestine Small	intestine
35	chr1:169862000-169863800	Active TSS	Fetal Kidney	kidney
36	chr1:169862000-169863800	Active TSS	Ovary	ovary
37	chr1:169862000-169863800	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr1:169862000-169863800	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr1:169862000-169863800	Active TSS	A549	lung
40	chr1:169862000-169864000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:169862000-169864000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:169862000-169864000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:169862000-169864000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:169862000-169864000	Active TSS	Pancreas	Pancrea
45	chr1:169862000-169864200	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr1:169862000-169864200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:169862200-169863800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:169862200-169863800	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr1:169862200-169863800	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr1:169862200-169863800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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