Variant report

Variant	rs28365885
Chromosome Location	chr12:49658537-49658538
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	SMARCB1	chr12:49658079-49660047	Hela-S3	cervix:	n/a	chr12:49658195-49658204 chr12:49659435-49659444
2	MAX	chr12:49657944-49659770	HCT-116	colon:	n/a	chr12:49658382-49658392 chr12:49658811-49658820 chr12:49658810-49658821
3	POLR2A	chr12:49658109-49660531	MCF10A-Er-Src	breast:	n/a	n/a
4	EGR1	chr12:49658130-49659005	K562	blood:	n/a	chr12:49658469-49658483 chr12:49658471-49658481 chr12:49658471-49658480 chr12:49658467-49658481 chr12:49658371-49658384 chr12:49658470-49658483 chr12:49658470-49658483 chr12:49658470-49658483 chr12:49658471-49658481 chr12:49658471-49658482 chr12:49658799-49658809 chr12:49658718-49658731 chr12:49658470-49658483 chr12:49658469-49658484 chr12:49658465-49658487
5	HA-E2F1	chr12:49658014-49660385	MCF-7	breast:	n/a	chr12:49658717-49658726 chr12:49658702-49658711
6	EGR1	chr12:49658217-49658753	GM12878	blood:	n/a	chr12:49658469-49658483 chr12:49658471-49658481 chr12:49658471-49658480 chr12:49658467-49658481 chr12:49658371-49658384 chr12:49658470-49658483 chr12:49658470-49658483 chr12:49658470-49658483 chr12:49658471-49658481 chr12:49658471-49658482 chr12:49658718-49658731 chr12:49658470-49658483 chr12:49658469-49658484 chr12:49658465-49658487
7	TAF1	chr12:49658522-49659079	GM12891	blood:	n/a	n/a
8	EP300	chr12:49658044-49659813	ECC-1	luminal epithelium:	n/a	chr12:49658274-49658290 chr12:49658361-49658377 chr12:49658774-49658790
9	ZBTB7A	chr12:49658411-49658677	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:49658068-49661661	K562	blood:	n/a	n/a
11	MAX	chr12:49658426-49659077	K562	blood:	n/a	chr12:49658811-49658820 chr12:49658810-49658821
12	SPI1	chr12:49658499-49658733	K562	blood:	n/a	n/a
13	MYC	chr12:49657953-49660107	A549	lung:	n/a	chr12:49658382-49658392 chr12:49658811-49658820 chr12:49658810-49658821
14	MAX	chr12:49658340-49659559	GM12878	blood:	n/a	chr12:49658382-49658392 chr12:49658811-49658820 chr12:49658810-49658821
15	MTA3	chr12:49657994-49659777	GM12878	blood:	n/a	n/a
16	FOXM1	chr12:49657916-49659811	ECC-1	luminal epithelium:	n/a	n/a
17	ELF1	chr12:49658080-49659862	MCF-7	breast:	n/a	chr12:49658343-49658352 chr12:49658266-49658278
18	POLR2A	chr12:49658245-49659569	A549	lung:	n/a	n/a
19	TAF1	chr12:49658280-49659601	H1-hESC	embryonic stem cell:	n/a	n/a
20	SPI1	chr12:49658503-49658700	K562	blood:	n/a	n/a
21	POLR2A	chr12:49658351-49664605	U87	brain:	n/a	n/a
22	MYC	chr12:49658497-49659034	MCF-7	breast:	n/a	chr12:49658811-49658820 chr12:49658810-49658821
23	RELA	chr12:49658435-49659580	GM19193	blood:	n/a	n/a
24	MAZ	chr12:49658060-49659613	GM12878	blood:	n/a	chr12:49658382-49658392 chr12:49658811-49658820 chr12:49658810-49658821
25	TBL1XR1	chr12:49658136-49659345	GM12878	blood:	n/a	n/a
26	NR2F2	chr12:49658022-49659942	MCF-7	breast:	n/a	n/a
27	PAX5	chr12:49658271-49659153	GM12878	blood:	n/a	n/a
28	EP300	chr12:49658078-49659647	K562	blood:	n/a	chr12:49658274-49658290 chr12:49658361-49658377 chr12:49658774-49658790
29	POLR2A	chr12:49658117-49661692	IMR90	lung:	n/a	n/a
30	POLR2A	chr12:49658000-49659860	HUVEC	blood vessel:	n/a	n/a
31	SIN3A	chr12:49658339-49659632	GM12878	blood:	n/a	chr12:49659448-49659461 chr12:49658738-49658749 chr12:49659043-49659056 chr12:49659055-49659068
32	POLR2A	chr12:49658070-49661060	Hela-S3	cervix:	n/a	n/a
33	SPI1	chr12:49658097-49659173	HL-60	blood:	n/a	chr12:49658489-49658502
34	NR2F2	chr12:49657924-49659910	K562	blood:	n/a	n/a
35	CTCF	chr12:49658400-49658550	NHEK	skin:	n/a	chr12:49658516-49658529
36	SIN3A	chr12:49658056-49659644	H1-hESC	embryonic stem cell:	n/a	chr12:49659448-49659461 chr12:49658738-49658749 chr12:49659043-49659056 chr12:49659055-49659068
37	YY1	chr12:49658159-49659624	K562	blood:	n/a	chr12:49658264-49658278 chr12:49658258-49658272 chr12:49658265-49658279
38	ZNF143	chr12:49658168-49659541	Hela-S3	cervix:	n/a	chr12:49658742-49658752
39	POLR2A	chr12:49658108-49660101	MCF10A-Er-Src	breast:	n/a	n/a
40	SRF	chr12:49658246-49659748	ECC-1	luminal epithelium:	n/a	n/a
41	ZBTB7A	chr12:49658041-49659307	ECC-1	luminal epithelium:	n/a	chr12:49658718-49658727
42	USF1	chr12:49658426-49659061	K562	blood:	n/a	n/a
43	ELF1	chr12:49658191-49659524	GM12878	blood:	n/a	chr12:49658343-49658352 chr12:49658266-49658278
44	RELA	chr12:49658178-49659662	GM12891	blood:	n/a	n/a
45	POLR2A	chr12:49658001-49664653	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr12:49657862-49669371	K562	blood:	n/a	n/a
47	CREB1	chr12:49658447-49659035	H1-hESC	embryonic stem cell:	n/a	n/a
48	HEY1	chr12:49658176-49659712	HepG2	liver:	n/a	chr12:49658259-49658274 chr12:49658377-49658392 chr12:49658382-49658397 chr12:49658811-49658820
49	CHD2	chr12:49658525-49659594	K562	blood:	n/a	n/a
50	POLR2A	chr12:49658165-49659939	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49657860..49660302-chr12:49730399..49733232,3	K562	blood:
2	chr12:49656742..49663815-chr12:49736558..49745017,19	MCF-7	breast:
3	chr12:49434105..49437855-chr12:49658238..49660568,3	K562	blood:
4	chr12:49523107..49527860-chr12:49656151..49664210,14	MCF-7	breast:
5	chr12:49519590..49527322-chr12:49655772..49662610,57	K562	blood:
6	chr12:49656587..49660636-chr12:49733539..49743833,13	K562	blood:
7	chr12:49581145..49584248-chr12:49657471..49660758,4	K562	blood:
8	chr12:49462455..49464108-chr12:49657502..49660398,3	K562	blood:
9	chr12:49658459..49659412-chr5:95067076..95067650,2	Hela-S3	cervix:
10	chr12:49657320..49660807-chr12:49714613..49719662,6	K562	blood:
11	chr12:49487580..49490269-chr12:49658075..49660760,2	K562	blood:
12	chr12:49448896..49462070-chr12:49656751..49663992,28	K562	blood:
13	chr12:49483859..49487327-chr12:49657616..49660606,5	K562	blood:
14	chr12:49519914..49528393-chr12:49656527..49662615,75	K562	blood:
15	chr12:49501897..49506471-chr12:49657604..49660787,6	MCF-7	breast:
16	chr12:49658471..49659400-chr3:169482442..169482984,2	Hela-S3	cervix:
17	chr12:49657692..49659587-chr12:49716247..49718208,2	MCF-7	breast:
18	chr1:94344587..94345216-chr12:49658330..49658949,2	NB4	blood:
19	chr12:49656786..49659396-chr6:114291007..114293085,2	MCF-7	breast:
20	chr12:49499760..49506124-chr12:49657415..49661017,8	K562	blood:
21	chr12:49462406..49465445-chr12:49657502..49661212,4	K562	blood:
22	chr12:49207714..49211177-chr12:49657864..49661147,3	K562	blood:
23	chr12:49657748..49660512-chr12:49730264..49732689,3	MCF-7	breast:
24	chr12:49412238..49414069-chr12:49657738..49659294,2	MCF-7	breast:
25	chr12:49657699..49660591-chr12:49932809..49935394,2	MCF-7	breast:
26	chr12:49619902..49623805-chr12:49655877..49662372,6	K562	blood:
27	chr12:49658449..49659329-chr3:156878118..156878938,3	Hela-S3	cervix:
28	chr12:49657602..49660330-chr12:50012266..50014334,2	K562	blood:
29	chr1:222885333..222885935-chr12:49658514..49659295,2	Hela-S3	cervix:
30	chr12:49658453..49658974-chr17:8076499..8077198,2	Hela-S3	cervix:
31	chr12:49654800..49660850-chr12:49685742..49692441,19	MCF-7	breast:
32	chr12:49496967..49499814-chr12:49657721..49660285,2	MCF-7	breast:
33	chr12:49658461..49659342-chr19:49990587..49991568,2	Hela-S3	cervix:
34	chr12:49390613..49393583-chr12:49657516..49659698,3	K562	blood:
35	chr12:49656589..49659420-chr13:91999028..92001178,2	K562	blood:
36	chr12:49449335..49458365-chr12:49656751..49666981,25	K562	blood:
37	chr12:49657419..49659044-chr4:71567380..71569012,2	MCF-7	breast:
38	chr12:49109310..49111237-chr12:49657606..49659331,2	K562	blood:
39	chr12:49657190..49661099-chr12:49688432..49694179,9	K562	blood:
40	chr12:49658462..49659340-chr17:45727327..45727843,2	HCT-116	colon:
41	chr1:109289222..109289740-chr12:49658263..49659046,2	Hela-S3	cervix:
42	chr12:49390613..49392741-chr12:49658198..49660350,2	K562	blood:
43	chr12:49656837..49661590-chr12:49759665..49765017,7	K562	blood:
44	chr12:49658339..49661093-chr12:49961458..49963113,2	MCF-7	breast:
45	chr12:49658305..49660610-chr22:29700972..29702617,2	K562	blood:
46	chr12:49658435..49659233-chr16:57835753..57836423,2	Hela-S3	cervix:
47	chr12:49410141..49415550-chr12:49657481..49661686,9	K562	blood:
48	chr12:49580809..49583875-chr12:49657471..49661424,5	K562	blood:
49	chr11:62608601..62609628-chr12:49658414..49658943,3	NB4	blood:
50	chr12:49658135..49661109-chr12:50235815..50238160,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TUBA1A-1	chr12:49658436-49658539	ENSG00000258101.1

Variant related genes	Relation type
TUBA1C	TF binding region
ENSG00000186666	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000172244	Chromatin interaction
ENSG00000067334	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000204173	Chromatin interaction
ENSG00000139549	Chromatin interaction
ENSG00000124151	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000102265	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000207058	Chromatin interaction
ENSG00000186063	Chromatin interaction
ENSG00000228775	Chromatin interaction
ENSG00000119522	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000258104	Chromatin interaction
ENSG00000207448	Chromatin interaction
ENSG00000215417	Chromatin interaction
ENSG00000167550	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000185340	Chromatin interaction
ENSG00000116266	Chromatin interaction
ENSG00000228624	Chromatin interaction
ENSG00000166912	Chromatin interaction
ENSG00000059769	Chromatin interaction
ENSG00000140859	Chromatin interaction
ENSG00000132676	Chromatin interaction
ENSG00000182934	Chromatin interaction
ENSG00000167552	Chromatin interaction
ENSG00000181418	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000248240	Chromatin interaction
ENSG00000162819	Chromatin interaction
ENSG00000067082	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000204387	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000170606	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000270141	Chromatin interaction
ENSG00000119280	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000244115	Chromatin interaction
ENSG00000164292	Chromatin interaction
ENSG00000200463	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000201823	Chromatin interaction
ENSG00000142541	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000106028	Chromatin interaction
ENSG00000078304	Chromatin interaction
ENSG00000108424	Chromatin interaction
ENSG00000129315	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000135519	Chromatin interaction
ENSG00000257913	Chromatin interaction
ENSG00000196591	Chromatin interaction
ENSG00000178401	Chromatin interaction
ENSG00000110074	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000163374	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000224892	Chromatin interaction
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11168952	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168953	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168954	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168955	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11542115	1.00[ASN][1000 genomes]
rs12310093	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759170	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59965487	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73306246	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49657000-49660200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:49657000-49660200	Active TSS	HSMM	muscle
3	chr12:49657200-49659000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:49657200-49659600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:49657200-49660200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr12:49657200-49660400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:49657200-49660600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr12:49657400-49659000	Bivalent Enhancer	Fetal Brain Male	brain
9	chr12:49657400-49659400	Active TSS	Rectal Smooth Muscle	rectum
10	chr12:49657400-49659800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:49657400-49660200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:49657600-49659400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:49657600-49659600	Active TSS	Muscle Satellite Cultured Cells	--
14	chr12:49657600-49659800	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr12:49657600-49659800	Active TSS	HMEC	breast
16	chr12:49657600-49660000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:49657600-49660200	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr12:49657600-49660400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:49657600-49660400	Active TSS	NHDF-Ad	bronchial
20	chr12:49657600-49660400	Active TSS	NHLF	lung
21	chr12:49657600-49660600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:49657600-49660600	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr12:49657600-49661000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr12:49657600-49661000	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr12:49657800-49659000	Active TSS	A549	lung
26	chr12:49657800-49659000	Active TSS	HepG2	liver
27	chr12:49657800-49659200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:49657800-49659400	Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr12:49657800-49659400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:49657800-49659400	Active TSS	Fetal Intestine Small	intestine
31	chr12:49657800-49659600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:49657800-49659600	Active TSS	Fetal Intestine Large	intestine
33	chr12:49657800-49659600	Active TSS	Fetal Lung	lung
34	chr12:49657800-49659800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:49657800-49660000	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr12:49657800-49660000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:49657800-49660200	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr12:49657800-49660200	Active TSS	GM12878-XiMat	blood
39	chr12:49657800-49660200	Active TSS	Osteobl	bone
40	chr12:49657800-49660400	Active TSS	H1 Cell Line	embryonic stem cell
41	chr12:49657800-49660400	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr12:49657800-49660400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:49657800-49660400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:49657800-49660400	Active TSS	Duodenum Mucosa	Duodenum
45	chr12:49657800-49660400	Active TSS	K562	blood
46	chr12:49657800-49660600	Active TSS	H9 Cell Line	embryonic stem cell
47	chr12:49657800-49660600	Active TSS	Hela-S3	cervix
48	chr12:49658000-49658600	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr12:49658000-49658800	Active TSS	Brain Hippocampus Middle	brain
50	chr12:49658000-49659000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle

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