Variant report

Variant	rs60396934
Chromosome Location	chr12:56509845-56509846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:118)
CpG islands
(count:0)
Chromatin interactive
region (count:45)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:118 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr12:56509830-56511379	K562	blood:	n/a	chr12:56510339-56510354
2	POLR2A	chr12:56508868-56512664	HepG2	liver:	n/a	n/a
3	HCFC1	chr12:56509842-56510763	K562	blood:	n/a	n/a
4	SP1	chr12:56509604-56511224	A549	lung:	n/a	chr12:56510326-56510338 chr12:56510326-56510338 chr12:56510326-56510337 chr12:56510327-56510336
5	SP1	chr12:56509591-56510893	A549	lung:	n/a	chr12:56510326-56510338 chr12:56510326-56510338 chr12:56510326-56510337 chr12:56510327-56510336
6	ELF1	chr12:56509837-56510987	MCF-7	breast:	n/a	chr12:56510355-56510368 chr12:56510358-56510367 chr12:56510357-56510368 chr12:56510357-56510368
7	POLR2A	chr12:56509642-56509907	HL-60	blood:	n/a	n/a
8	CREB1	chr12:56509619-56510974	HepG2	liver:	n/a	n/a
9	E2F6	chr12:56509725-56509870	K562	blood:	n/a	n/a
10	CREB1	chr12:56509571-56511357	GM12878	blood:	n/a	n/a
11	E2F4	chr12:56509644-56510617	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr12:56508873-56512706	U87	brain:	n/a	n/a
13	PAX5	chr12:56509682-56509916	GM12878	blood:	n/a	n/a
14	TAF1	chr12:56509481-56509910	H1-hESC	embryonic stem cell:	n/a	n/a
15	TAF1	chr12:56509473-56511034	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr12:56509084-56511359	HUVEC	blood vessel:	n/a	n/a
17	GABPA	chr12:56509706-56510912	SK-N-SH	brain:	n/a	chr12:56510358-56510365
18	POLR2A	chr12:56509709-56509883	H1-hESC	embryonic stem cell:	n/a	n/a
19	SIN3AK20	chr12:56509811-56510887	MCF-7	breast:	n/a	n/a
20	POLR2A	chr12:56508976-56509891	MCF-7	breast:	n/a	n/a
21	POLR2A	chr12:56508985-56513679	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr12:56509088-56509911	HCT-116	colon:	n/a	n/a
23	GABPA	chr12:56509458-56511073	A549	lung:	n/a	chr12:56510358-56510365
24	GABPA	chr12:56509579-56510924	MCF-7	breast:	n/a	chr12:56510358-56510365
25	REST	chr12:56509398-56511321	A549	lung:	n/a	chr12:56510197-56510204
26	POLR2A	chr12:56507127-56512673	PFSK-1	brain:	n/a	n/a
27	GABPA	chr12:56509726-56510875	SK-N-SH	brain:	n/a	chr12:56510358-56510365
28	BCL3	chr12:56509818-56511375	A549	lung:	n/a	chr12:56510359-56510368
29	POLR2A	chr12:56509616-56509922	HCT-116	colon:	n/a	n/a
30	CREB1	chr12:56509704-56511069	ECC-1	luminal epithelium:	n/a	n/a
31	SETDB1	chr12:56507833-56510301	K562	blood:	n/a	chr12:56510089-56510113
32	YY1	chr12:56509629-56510888	SK-N-SH_RA	brain:	n/a	chr12:56510068-56510078
33	POLR2A	chr12:56509776-56512585	GM19099	blood:	n/a	n/a
34	GABPA	chr12:56509771-56511227	HL-60	blood:	n/a	chr12:56510358-56510365
35	FOXM1	chr12:56509632-56510945	GM12878	blood:	n/a	n/a
36	YY1	chr12:56509677-56509915	GM12891	blood:	n/a	n/a
37	TCF12	chr12:56509725-56511388	ECC-1	luminal epithelium:	n/a	n/a
38	TAF1	chr12:56509523-56511283	ECC-1	luminal epithelium:	n/a	n/a
39	MAX	chr12:56509555-56511363	ECC-1	luminal epithelium:	n/a	n/a
40	MAX	chr12:56509565-56511085	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr12:56509008-56512584	PANC-1	pancreas:	n/a	n/a
42	MAX	chr12:56509677-56510852	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr12:56508835-56512388	MCF10A-Er-Src	breast:	n/a	n/a
44	YY1	chr12:56509626-56510964	ECC-1	luminal epithelium:	n/a	chr12:56510068-56510078
45	POLR2A	chr12:56509734-56509894	ProgFib	skin:	n/a	n/a
46	POLR2A	chr12:56509530-56509925	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr12:56509450-56511358	HUVEC	blood vessel:	n/a	n/a
48	MYC	chr12:56509842-56509882	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr12:56509724-56509904	A549	lung:	n/a	n/a
50	POLR2A	chr12:56509640-56512560	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:45 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56388663..56390972-chr12:56509029..56512021,2	K562	blood:
2	chr12:56364310..56368149-chr12:56508797..56512267,4	K562	blood:
3	chr12:56471198..56482935-chr12:56506922..56516262,73	MCF-7	breast:
4	chr12:56434006..56443603-chr12:56507645..56514884,44	K562	blood:
5	chr12:56507991..56525761-chr12:56579808..56586137,68	MCF-7	breast:
6	chr12:56509755..56511987-chr12:56606090..56607833,2	MCF-7	breast:
7	chr12:56509568..56510514-chrX:110924319..110925161,2	Hela-S3	cervix:
8	chr11:62521318..62521847-chr12:56509792..56510749,2	NB4	blood:
9	chr12:56390988..56392833-chr12:56509534..56511821,2	K562	blood:
10	chr12:56470948..56480058-chr12:56507665..56513741,17	K562	blood:
11	chr12:56433777..56443620-chr12:56502225..56514736,38	MCF-7	breast:
12	chr12:56508832..56515879-chr12:56578376..56587782,37	MCF-7	breast:
13	chr12:56433331..56443603-chr12:56506173..56514581,35	K562	blood:
14	chr12:56508592..56516532-chr12:56613723..56619321,16	MCF-7	breast:
15	chr12:56509088..56512395-chr12:56615837..56618663,6	MCF-7	breast:
16	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
17	chr12:56485826..56488734-chr12:56509000..56512057,4	MCF-7	breast:
18	chr12:56508549..56510968-chr12:56650635..56652672,2	K562	blood:
19	chr12:56364840..56368363-chr12:56508725..56511034,3	MCF-7	breast:
20	chr12:56365214..56370075-chr12:56508797..56513405,7	K562	blood:
21	chr12:56509109..56511870-chr12:58238772..58240512,2	MCF-7	breast:
22	chr12:56509009..56513573-chr12:56543891..56549811,15	MCF-7	breast:
23	chr12:56509108..56511988-chr12:56607579..56610265,3	MCF-7	breast:
24	chr12:56509686..56511779-chr12:56864045..56866369,2	MCF-7	breast:
25	chr12:56120734..56123554-chr12:56508983..56512643,4	K562	blood:
26	chr12:56120240..56124369-chr12:56508983..56513755,7	K562	blood:
27	chr12:56509186..56511595-chr17:57696618..57699149,2	MCF-7	breast:
28	chr12:56509168..56511032-chr8:89338903..89341041,2	MCF-7	breast:
29	chr12:56384934..56392097-chr12:56507991..56512680,9	MCF-7	breast:
30	chr12:56509253..56512129-chr20:48805699..48808212,2	MCF-7	breast:
31	chr12:56433908..56446518-chr12:56506026..56517165,55	MCF-7	breast:
32	chr12:56508809..56510764-chr12:56599083..56602817,4	K562	blood:
33	chr12:56509441..56516191-chr12:56612345..56620104,13	K562	blood:
34	chr12:56509416..56511778-chr7:5467782..5470383,2	MCF-7	breast:
35	chr12:56390533..56392803-chr12:56508864..56512540,5	K562	blood:
36	chr12:56509359..56512044-chr12:56694319..56695939,2	MCF-7	breast:
37	chr12:56508870..56510876-chr8:144821335..144824118,2	MCF-7	breast:
38	chr12:56509293..56514359-chr12:56692717..56696999,9	K562	blood:
39	chr12:56122088..56125310-chr12:56509016..56512267,4	MCF-7	breast:
40	chr1:45196194..45197403-chr12:56509799..56510805,4	Hela-S3	cervix:
41	chr12:56509603..56512035-chr12:57038748..57040490,2	K562	blood:
42	chr12:56415006..56416530-chr12:56508987..56510666,2	K562	blood:
43	chr12:56507747..56515530-chr12:56549896..56559767,36	MCF-7	breast:
44	chr12:56509092..56510764-chr12:56601288..56602817,2	K562	blood:
45	chr12:56346732..56350497-chr12:56509495..56512206,3	MCF-7	breast:

No data

Variant related genes	Relation type
RPL41	TF binding region
ESYT1	TF binding region
ENSG00000257553	TF binding region
ZC3H10	TF binding region
ENSG00000156103	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000255990	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000185670	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000101901	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000172216	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000207031	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000110955	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000203499	Chromatin interaction
ENSG00000141367	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000273084	Chromatin interaction
ENSG00000234432	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000135423	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000253553	Chromatin interaction
ENSG00000139641	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10876878	0.83[ASN][1000 genomes]
rs11171752	0.94[ASN][1000 genomes]
rs11171772	0.83[ASN][1000 genomes]
rs11834728	1.00[ASN][1000 genomes]
rs12320265	0.83[ASN][1000 genomes]
rs1274502	0.83[ASN][1000 genomes]
rs1274503	0.83[ASN][1000 genomes]
rs1405859	0.83[ASN][1000 genomes]
rs17118333	1.00[ASN][1000 genomes]
rs2271188	1.00[ASN][1000 genomes]
rs2271190	1.00[ASN][1000 genomes]
rs2271192	0.94[ASN][1000 genomes]
rs2463365	0.83[ASN][1000 genomes]
rs2629451	0.83[ASN][1000 genomes]
rs2629453	0.83[ASN][1000 genomes]
rs2695783	0.83[ASN][1000 genomes]
rs2695784	0.83[ASN][1000 genomes]
rs28676339	1.00[ASN][1000 genomes]
rs2930788	0.83[ASN][1000 genomes]
rs2950573	0.83[ASN][1000 genomes]
rs3759096	1.00[ASN][1000 genomes]
rs3802996	1.00[ASN][1000 genomes]
rs3809130	1.00[ASN][1000 genomes]
rs55887836	0.93[ASN][1000 genomes]
rs56851901	1.00[ASN][1000 genomes]
rs57280585	1.00[ASN][1000 genomes]
rs58009483	0.83[ASN][1000 genomes]
rs58476735	1.00[ASN][1000 genomes]
rs58548156	1.00[ASN][1000 genomes]
rs58663297	1.00[ASN][1000 genomes]
rs59053322	0.83[ASN][1000 genomes]
rs59078852	0.83[ASN][1000 genomes]
rs59966703	0.83[ASN][1000 genomes]
rs61939011	0.83[ASN][1000 genomes]
rs703823	0.83[ASN][1000 genomes]
rs7489249	0.83[ASN][1000 genomes]
rs773654	0.83[ASN][1000 genomes]
rs773658	0.83[ASN][1000 genomes]
rs773659	0.83[ASN][1000 genomes]
rs773661	0.83[ASN][1000 genomes]
rs7962107	0.83[ASN][1000 genomes]
rs7967464	0.83[ASN][1000 genomes]
rs7975405	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 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	chr12:56506600-56510000	Weak transcription	Gastric	stomach
2	chr12:56507600-56510000	Weak transcription	Spleen	Spleen
3	chr12:56508400-56510000	Weak transcription	K562	blood
4	chr12:56509000-56510400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:56509000-56510600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr12:56509000-56510600	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr12:56509000-56510800	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr12:56509000-56510800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr12:56509000-56511000	Active TSS	H1 Cell Line	embryonic stem cell
10	chr12:56509000-56511600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:56509000-56512400	Active TSS	Brain Angular Gyrus	brain
12	chr12:56509000-56512800	Active TSS	H9 Cell Line	embryonic stem cell
13	chr12:56509000-56513400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr12:56509200-56510600	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr12:56509200-56510800	Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr12:56509200-56511000	Active TSS	Brain Cingulate Gyrus	brain
17	chr12:56509200-56511000	Active TSS	Fetal Brain Female	brain
18	chr12:56509200-56511000	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr12:56509200-56511000	Active TSS	HSMM	muscle
20	chr12:56509200-56511600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:56509200-56512400	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr12:56509200-56512600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:56509200-56512600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:56509200-56512600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:56509200-56512600	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr12:56509200-56512800	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr12:56509200-56513000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:56509200-56513000	Active TSS	Lung	lung
29	chr12:56509400-56510200	Active TSS	Fetal Brain Male	brain
30	chr12:56509400-56510800	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr12:56509400-56510800	Active TSS	A549	lung
32	chr12:56509400-56511000	Active TSS	Brain Germinal Matrix	brain
33	chr12:56509400-56511000	Active TSS	NHEK	skin
34	chr12:56509400-56511200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:56509400-56511600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:56509400-56511600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:56509400-56511600	Active TSS	Brain Anterior Caudate	brain
38	chr12:56509400-56511600	Active TSS	Brain Hippocampus Middle	brain
39	chr12:56509400-56511600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:56509400-56511600	Active TSS	Brain Substantia Nigra	brain
41	chr12:56509400-56511600	Active TSS	Duodenum Mucosa	Duodenum
42	chr12:56509400-56511600	Active TSS	Fetal Intestine Large	intestine
43	chr12:56509400-56511600	Active TSS	Placenta	Placenta
44	chr12:56509400-56511600	Active TSS	Rectal Smooth Muscle	rectum
45	chr12:56509400-56511600	Active TSS	Right Atrium	heart
46	chr12:56509400-56511600	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr12:56509400-56511600	Active TSS	Stomach Mucosa	stomach
48	chr12:56509400-56511600	Active TSS	Stomach Smooth Muscle	stomach
49	chr12:56509400-56512200	Active TSS	Fetal Muscle Trunk	muscle
50	chr12:56509400-56512200	Active TSS	HMEC	breast

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