Variant report

Variant	rs17300712
Chromosome Location	chr1:180472511-180472512
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	SP1	chr1:180471121-180472604	A549	lung:	n/a	chr1:180471962-180471971 chr1:180471962-180471972 chr1:180471558-180471571 chr1:180471964-180471978 chr1:180471961-180471972
2	ELK1	chr1:180471718-180472511	K562	blood:	n/a	n/a
3	FOXA1	chr1:180472110-180472637	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:180471108-180472708	HCT-116	colon:	n/a	n/a
5	POLR2A	chr1:180472419-180472708	Hela-S3	cervix:	n/a	n/a
6	TCF12	chr1:180470984-180472590	A549	lung:	n/a	chr1:180472228-180472235
7	POLR2A	chr1:180471266-180472720	K562	blood:	n/a	n/a
8	TCF7L2	chr1:180471096-180472758	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:180470958-180472516	GM12892	blood:	n/a	n/a
10	POLR2A	chr1:180471124-180472614	GM15510	blood:	n/a	n/a
11	MAX	chr1:180471019-180472842	HepG2	liver:	n/a	chr1:180471542-180471551 chr1:180472613-180472622
12	ATF2	chr1:180471550-180472661	GM12878	blood:	n/a	n/a
13	STAT1	chr1:180472506-180472561	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:180471062-180472713	K562	blood:	n/a	n/a
15	PML	chr1:180471208-180472671	K562	blood:	n/a	n/a
16	RUNX3	chr1:180471166-180472678	GM12878	blood:	n/a	n/a
17	TBP	chr1:180471024-180472964	Hela-S3	cervix:	n/a	n/a
18	MAFK	chr1:180471301-180472616	K562	blood:	n/a	n/a
19	FOXA2	chr1:180472193-180472622	HepG2	liver:	n/a	n/a
20	GABPA	chr1:180471483-180472885	HL-60	blood:	n/a	chr1:180471809-180471823
21	GABPA	chr1:180470962-180472801	MCF-7	breast:	n/a	chr1:180471809-180471823
22	BHLHE40	chr1:180471000-180472525	K562	blood:	n/a	chr1:180471536-180471557 chr1:180471542-180471551 chr1:180471540-180471553 chr1:180471542-180471551 chr1:180471543-180471552
23	POLR2A	chr1:180470946-180472536	SK-N-MC	brain:	n/a	n/a
24	MYC	chr1:180471203-180472858	K562	blood:	n/a	chr1:180471542-180471551 chr1:180472613-180472622
25	POLR2A	chr1:180471001-180472888	GM12891	blood:	n/a	n/a
26	BRCA1	chr1:180471927-180472563	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:180470947-180472549	GM12892	blood:	n/a	n/a
28	CTCF	chr1:180471514-180472561	K562	blood:	n/a	n/a
29	POLR2A	chr1:180471172-180472674	K562	blood:	n/a	n/a
30	TBL1XR1	chr1:180471156-180472561	K562	blood:	n/a	n/a
31	UBTF	chr1:180471116-180472604	K562	blood:	n/a	n/a
32	MYC	chr1:180471219-180472576	K562	blood:	n/a	chr1:180471542-180471551
33	POLR2A	chr1:180471149-180472659	GM12891	blood:	n/a	n/a
34	POLR2A	chr1:180471040-180472676	GM12892	blood:	n/a	n/a
35	MTA3	chr1:180470923-180472729	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:180471170-180472604	GM12878	blood:	n/a	n/a
37	ZKSCAN1	chr1:180471105-180472854	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr1:180471022-180473009	HUVEC	blood vessel:	n/a	n/a
39	SMARCC1	chr1:180471116-180472763	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr1:180471051-180472723	K562	blood:	n/a	n/a
41	CEBPB	chr1:180471468-180472715	GM12878	blood:	n/a	n/a
42	USF2	chr1:180471179-180472719	Hela-S3	cervix:	n/a	chr1:180471536-180471557 chr1:180471542-180471551 chr1:180471540-180471553 chr1:180471542-180471551 chr1:180471541-180471552 chr1:180471543-180471552
43	FOXA2	chr1:180471394-180472851	A549	lung:	n/a	n/a
44	POLR2A	chr1:180470979-180472871	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr1:180471099-180472729	Hela-S3	cervix:	n/a	n/a
46	TAF1	chr1:180472465-180472654	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr1:180471075-180472807	Raji	blood:	n/a	n/a
48	NFIC	chr1:180471259-180472533	GM12878	blood:	n/a	n/a
49	MAFK	chr1:180471184-180472765	Hela-S3	cervix:	n/a	n/a
50	USF1	chr1:180470938-180472749	HCT-116	colon:	n/a	chr1:180471536-180471557 chr1:180471542-180471551 chr1:180471540-180471553 chr1:180471542-180471551 chr1:180471541-180471552 chr1:180471543-180471552

No.	Distal block	Cell Line	Cell type
1	chr1:180470530..180472800-chr1:181059348..181062070,2	MCF-7	breast:
2	chr1:180470531..180473320-chr1:180599332..180602016,2	K562	blood:
3	chr1:180472105..180473813-chr1:181057993..181060465,2	K562	blood:
4	chr1:179922809..179925375-chr1:180469288..180472844,3	MCF-7	breast:
5	chr1:180470493..180473506-chr1:180597830..180602116,4	MCF-7	breast:
6	chr1:180471780..180472722-chr21:36260550..36261373,2	Hela-S3	cervix:
7	chr1:180470101..180473441-chr1:181055955..181060608,7	K562	blood:
8	chr1:180471844..180473549-chr1:182806960..182809531,2	MCF-7	breast:
9	chr1:145382428..145382959-chr1:180471816..180472628,2	Hela-S3	cervix:
10	chr1:180470962..180473881-chr1:180832608..180834765,2	MCF-7	breast:
11	chr1:180197528..180200245-chr1:180468948..180472883,3	MCF-7	breast:
12	chr1:179869245..179870791-chr1:180471258..180473082,2	MCF-7	breast:

Variant related genes	Relation type
ACBD6	TF binding region
ENSG00000159216	Chromatin interaction
ENSG00000121454	Chromatin interaction
ENSG00000272198	Chromatin interaction
ENSG00000135829	Chromatin interaction
ENSG00000162783	Chromatin interaction
ENSG00000143324	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000264916	Chromatin interaction
ENSG00000233396	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000135837	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10914021	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10914022	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10914035	0.84[EUR][1000 genomes]
rs10914038	0.83[EUR][1000 genomes]
rs12027839	0.83[EUR][1000 genomes]
rs12027878	0.83[EUR][1000 genomes]
rs12039331	0.82[CEU][hapmap]
rs12044653	0.83[EUR][1000 genomes]
rs12045365	0.81[EUR][1000 genomes]
rs12407684	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13373944	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13374104	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13374665	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13376342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1416822	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16856127	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17300282	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17300340	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17300579	1.00[CEU][hapmap]
rs17300600	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17372281	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17372295	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17372362	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17372667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28816398	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4405110	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4446932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4651065	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4652509	0.83[EUR][1000 genomes]
rs56759227	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57537558	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57882351	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58047798	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58089956	0.83[EUR][1000 genomes]
rs58677059	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59022209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59113753	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59829460	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60927564	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6425643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6425646	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6672501	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6680668	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6694454	0.84[EUR][1000 genomes]
rs6694896	0.80[EUR][1000 genomes]
rs6697232	0.83[EUR][1000 genomes]
rs6702245	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6704001	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72713000	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72714804	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72714834	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72714847	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72714855	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72714856	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72714861	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72714864	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72714866	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72714870	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72714877	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72714879	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72714887	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72714902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72716607	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72716615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72716616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72716625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72716627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72716629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72716632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72720914	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132851	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74135185	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7517775	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7525689	0.92[EUR][1000 genomes]
rs7547266	0.90[EUR][1000 genomes]
rs946636	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs961162	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9650999	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
7	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180468200-180472600	Active TSS	GM12878-XiMat	blood
2	chr1:180470000-180472800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr1:180470200-180472600	Active TSS	Fetal Kidney	kidney
4	chr1:180470200-180472600	Active TSS	Fetal Lung	lung
5	chr1:180470200-180472800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr1:180470400-180472600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:180470400-180472600	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:180470400-180472600	Active TSS	Right Ventricle	heart
9	chr1:180470400-180472600	Active TSS	A549	lung
10	chr1:180470400-180472600	Active TSS	NHDF-Ad	bronchial
11	chr1:180470400-180472800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:180470400-180472800	Active TSS	HSMM	muscle
13	chr1:180470600-180472600	Active TSS	Fetal Intestine Small	intestine
14	chr1:180470600-180472800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:180470800-180472600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:180470800-180472600	Active TSS	Fetal Intestine Large	intestine
17	chr1:180470800-180472800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:180470800-180472800	Active TSS	Brain Germinal Matrix	brain
19	chr1:180470800-180472800	Active TSS	Brain Hippocampus Middle	brain
20	chr1:180470800-180472800	Active TSS	Fetal Muscle Trunk	muscle
21	chr1:180470800-180472800	Active TSS	Ovary	ovary
22	chr1:180470800-180472800	Active TSS	Pancreas	Pancrea
23	chr1:180470800-180472800	Active TSS	Psoas Muscle	Psoas
24	chr1:180471000-180472600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:180471000-180472600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:180471000-180472600	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr1:180471000-180472600	Active TSS	Esophagus	oesophagus
28	chr1:180471000-180472600	Active TSS	Left Ventricle	heart
29	chr1:180471000-180472600	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr1:180471000-180472600	Active TSS	Small Intestine	intestine
31	chr1:180471000-180472600	Active TSS	Stomach Mucosa	stomach
32	chr1:180471000-180472800	Active TSS	Aorta	Aorta
33	chr1:180471000-180472800	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr1:180471000-180473000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr1:180471200-180472600	Active TSS	Brain Substantia Nigra	brain
36	chr1:180471200-180472800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:180471200-180473000	Active TSS	Stomach Smooth Muscle	stomach
38	chr1:180471400-180472600	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr1:180472000-180472600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:180472000-180472800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr1:180472000-180472800	Active TSS	Right Atrium	heart
42	chr1:180472000-180473000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:180472200-180472600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:180472200-180472600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:180472200-180472600	Flanking Active TSS	Fetal Brain Female	brain
46	chr1:180472200-180472600	Flanking Active TSS	Fetal Heart	heart
47	chr1:180472200-180472800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:180472200-180472800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
49	chr1:180472200-180472800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr1:180472200-180472800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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