Variant report

Variant	rs2335453
Chromosome Location	chr12:49660371-49660372
allele	A/C
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	chr12:49658109-49660531	MCF10A-Er-Src	breast:	n/a	n/a
2	HA-E2F1	chr12:49658014-49660385	MCF-7	breast:	n/a	chr12:49658717-49658726 chr12:49658702-49658711
3	MXI1	chr12:49660195-49660414	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:49660211-49660658	GM12892	blood:	n/a	n/a
5	POLR2A	chr12:49658068-49661661	K562	blood:	n/a	n/a
6	POLR2A	chr12:49660345-49661089	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr12:49660199-49660635	HCT-116	colon:	n/a	n/a
8	POLR2A	chr12:49658351-49664605	U87	brain:	n/a	n/a
9	POLR2A	chr12:49660155-49660702	HL-60	blood:	n/a	n/a
10	SIN3AK20	chr12:49660113-49660437	A549	lung:	n/a	n/a
11	POLR2A	chr12:49660089-49660442	HepG2	liver:	n/a	n/a
12	POLR2A	chr12:49660229-49660702	MCF-7	breast:	n/a	n/a
13	POLR2A	chr12:49658117-49661692	IMR90	lung:	n/a	n/a
14	POLR2A	chr12:49658070-49661060	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr12:49660160-49662050	K562	blood:	n/a	n/a
16	MAX	chr12:49660115-49660642	K562	blood:	n/a	chr12:49660254-49660261 chr12:49660251-49660262 chr12:49660251-49660262 chr12:49660253-49660262 chr12:49660252-49660262 chr12:49660252-49660262 chr12:49660250-49660263 chr12:49660251-49660262 chr12:49660248-49660263 chr12:49660250-49660263 chr12:49660250-49660263 chr12:49660247-49660266 chr12:49660252-49660261 chr12:49660250-49660263 chr12:49660250-49660265
17	POLR2A	chr12:49658001-49664653	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr12:49657862-49669371	K562	blood:	n/a	n/a
19	POLR2A	chr12:49660311-49660601	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:49658069-49662113	K562	blood:	n/a	n/a
21	POLR2A	chr12:49660080-49661193	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr12:49660290-49660616	ECC-1	luminal epithelium:	n/a	n/a
23	MAX	chr12:49660122-49661264	A549	lung:	n/a	chr12:49660254-49660261 chr12:49660251-49660262 chr12:49660251-49660262 chr12:49660253-49660262 chr12:49660252-49660262 chr12:49660252-49660262 chr12:49660250-49660263 chr12:49660251-49660262 chr12:49660248-49660263 chr12:49660890-49660899 chr12:49660250-49660263 chr12:49660250-49660263 chr12:49660890-49660899 chr12:49660247-49660266 chr12:49660890-49660899 chr12:49660252-49660261 chr12:49660889-49660900 chr12:49660250-49660263 chr12:49660889-49660900 chr12:49660890-49660900 chr12:49660250-49660265
24	POLR2A	chr12:49660207-49662000	K562	blood:	n/a	n/a
25	POLR2A	chr12:49660073-49661228	HCT-116	colon:	n/a	n/a
26	ZNF263	chr12:49660216-49660611	HEK293-T-REx	kidney:	n/a	n/a
27	POLR2A	chr12:49660119-49662037	K562	blood:	n/a	n/a
28	POLR2A	chr12:49660194-49661761	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr12:49658159-49660776	HepG2	liver:	n/a	n/a
30	POLR2A	chr12:49660363-49660605	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr12:49660363-49660395	HepG2	liver:	n/a	n/a
32	MXI1	chr12:49660198-49660474	K562	blood:	n/a	n/a
33	POLR2A	chr12:49657881-49662104	U87	brain:	n/a	n/a
34	POLR2A	chr12:49657892-49662191	SK-N-MC	brain:	n/a	n/a
35	HEY1	chr12:49660069-49662204	K562	blood:	n/a	n/a
36	POLR2A	chr12:49658259-49660512	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr12:49660147-49662192	GM12878	blood:	n/a	n/a
38	ZNF384	chr12:49659335-49660467	K562	blood:	n/a	n/a
39	POLR2A	chr12:49660367-49660474	MCF-7	breast:	n/a	n/a
40	POLR2A	chr12:49657998-49661215	HUVEC	blood vessel:	n/a	n/a
41	HCFC1	chr12:49657918-49661243	Hela-S3	cervix:	n/a	n/a
42	MAX	chr12:49660094-49660411	NB4	blood:	n/a	chr12:49660254-49660261 chr12:49660251-49660262 chr12:49660251-49660262 chr12:49660253-49660262 chr12:49660252-49660262 chr12:49660252-49660262 chr12:49660250-49660263 chr12:49660251-49660262 chr12:49660248-49660263 chr12:49660250-49660263 chr12:49660250-49660263 chr12:49660247-49660266 chr12:49660252-49660261 chr12:49660250-49660263 chr12:49660250-49660265
43	ZKSCAN1	chr12:49660344-49660462	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr12:49660280-49660622	GM12878	blood:	n/a	n/a
45	POLR2A	chr12:49658323-49670206	PFSK-1	brain:	n/a	n/a
46	MAX	chr12:49660168-49661052	Hela-S3	cervix:	n/a	chr12:49660254-49660261 chr12:49660251-49660262 chr12:49660251-49660262 chr12:49660253-49660262 chr12:49660252-49660262 chr12:49660252-49660262 chr12:49660250-49660263 chr12:49660251-49660262 chr12:49660248-49660263 chr12:49660890-49660899 chr12:49660250-49660263 chr12:49660250-49660263 chr12:49660890-49660899 chr12:49660247-49660266 chr12:49660890-49660899 chr12:49660252-49660261 chr12:49660889-49660900 chr12:49660250-49660263 chr12:49660889-49660900 chr12:49660890-49660900 chr12:49660250-49660265
47	E2F6	chr12:49660341-49660474	K562	blood:	n/a	n/a
48	POLR2A	chr12:49660062-49661153	U87	brain:	n/a	n/a
49	POLR2A	chr12:49658134-49662185	GM12878	blood:	n/a	n/a
50	POLR2A	chr12:49660338-49660563	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49656742..49663815-chr12:49736558..49745017,19	MCF-7	breast:
2	chr12:49434105..49437855-chr12:49658238..49660568,3	K562	blood:
3	chr12:49658539..49660530-chr6:290672..293249,2	MCF-7	breast:
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	chr12:49657320..49660807-chr12:49714613..49719662,6	K562	blood:
10	chr12:49487580..49490269-chr12:49658075..49660760,2	K562	blood:
11	chr12:49659293..49661080-chr22:50961474..50964056,2	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	chr12:49446124..49447679-chr12:49658939..49661024,2	K562	blood:
16	chr12:49501897..49506471-chr12:49657604..49660787,6	MCF-7	breast:
17	chr12:49490563..49493344-chr12:49659510..49661117,2	K562	blood:
18	chr12:49499760..49506124-chr12:49657415..49661017,8	K562	blood:
19	chr12:49462406..49465445-chr12:49657502..49661212,4	K562	blood:
20	chr12:49658793..49660553-chr12:49719371..49721124,2	MCF-7	breast:
21	chr12:49207714..49211177-chr12:49657864..49661147,3	K562	blood:
22	chr12:49630703..49633435-chr12:49659066..49660626,2	MCF-7	breast:
23	chr12:49657748..49660512-chr12:49730264..49732689,3	MCF-7	breast:
24	chr12:49657699..49660591-chr12:49932809..49935394,2	MCF-7	breast:
25	chr12:49619902..49623805-chr12:49655877..49662372,6	K562	blood:
26	chr12:49654800..49660850-chr12:49685742..49692441,19	MCF-7	breast:
27	chr12:49435486..49438666-chr12:49658667..49660787,3	MCF-7	breast:
28	chr12:49578543..49581092-chr12:49658927..49660844,2	K562	blood:
29	chr12:49449335..49458365-chr12:49656751..49666981,25	K562	blood:
30	chr12:49658775..49661727-chr12:49715622..49718429,2	K562	blood:
31	chr12:49657190..49661099-chr12:49688432..49694179,9	K562	blood:
32	chr12:49659146..49661010-chr12:49813234..49815442,2	K562	blood:
33	chr12:49658877..49660532-chr12:49934682..49936960,2	K562	blood:
34	chr12:49351320..49352963-chr12:49659062..49660649,2	K562	blood:
35	chr12:49656837..49661590-chr12:49759665..49765017,7	K562	blood:
36	chr12:49658339..49661093-chr12:49961458..49963113,2	MCF-7	breast:
37	chr12:49658305..49660610-chr22:29700972..29702617,2	K562	blood:
38	chr12:49659194..49661044-chr17:57925096..57927054,2	MCF-7	breast:
39	chr12:49410141..49415550-chr12:49657481..49661686,9	K562	blood:
40	chr12:49580809..49583875-chr12:49657471..49661424,5	K562	blood:
41	chr12:49658135..49661109-chr12:50235815..50238160,2	MCF-7	breast:
42	chr12:49656722..49663896-chr12:49682381..49687774,8	K562	blood:
43	chr12:49522979..49526796-chr12:49655970..49661455,13	MCF-7	breast:
44	chr12:49658707..49660390-chr12:108955166..108956839,2	MCF-7	breast:
45	chr12:49657571..49662873-chr12:49757027..49762131,10	K562	blood:
46	chr12:49657208..49661363-chr12:49714955..49717990,5	MCF-7	breast:
47	chr12:49434105..49439097-chr12:49658238..49660568,5	K562	blood:
48	chr12:49453115..49455291-chr12:49657846..49660975,4	MCF-7	breast:
49	chr12:49657502..49660502-chr12:50135111..50136880,4	K562	blood:
50	chr12:49581100..49585285-chr12:49656726..49660800,10	MCF-7	breast:

Variant related genes	Relation type
TUBA1C	TF binding region
ENSG00000258101	TF binding region
ENSG00000257346	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000136003	Chromatin interaction
ENSG00000167552	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000110074	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000178401	Chromatin interaction
ENSG00000167550	Chromatin interaction
ENSG00000135519	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000112679	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000185340	Chromatin interaction
ENSG00000182934	Chromatin interaction
ENSG00000134287	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000130489	Chromatin interaction
ENSG00000272821	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000067082	Chromatin interaction
ENSG00000139549	Chromatin interaction
ENSG00000075856	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10783310	0.86[ASN][1000 genomes]
rs10875937	0.86[ASN][1000 genomes]
rs11168948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834543	0.83[ASN][1000 genomes]
rs17123623	0.82[ASN][1000 genomes]
rs7133057	0.82[ASN][1000 genomes]
rs7971455	0.81[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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49657200-49660400	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr12:49657200-49660600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:49657600-49660400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:49657600-49660400	Active TSS	NHDF-Ad	bronchial
5	chr12:49657600-49660400	Active TSS	NHLF	lung
6	chr12:49657600-49660600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:49657600-49660600	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr12:49657600-49661000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr12:49657600-49661000	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr12:49657800-49660400	Active TSS	H1 Cell Line	embryonic stem cell
11	chr12:49657800-49660400	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr12:49657800-49660400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:49657800-49660400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:49657800-49660400	Active TSS	Duodenum Mucosa	Duodenum
15	chr12:49657800-49660400	Active TSS	K562	blood
16	chr12:49657800-49660600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr12:49657800-49660600	Active TSS	Hela-S3	cervix
18	chr12:49658000-49660400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:49658000-49660800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:49658000-49660800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:49658000-49661400	Active TSS	HSMMtube	muscle
22	chr12:49658000-49661600	Active TSS	Esophagus	oesophagus
23	chr12:49658200-49660400	Active TSS	Colonic Mucosa	Colon
24	chr12:49658200-49660400	Active TSS	NH-A	brain
25	chr12:49658200-49660400	Active TSS	NHEK	skin
26	chr12:49658800-49660400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:49659000-49663200	Transcr. at gene 5' and 3'	A549	lung
28	chr12:49659200-49673600	Weak transcription	Fetal Brain Male	brain
29	chr12:49659400-49660400	Active TSS	Stomach Smooth Muscle	stomach
30	chr12:49659400-49660400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr12:49659400-49661800	Weak transcription	Brain Substantia Nigra	brain
32	chr12:49659400-49664200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:49659600-49660600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:49659600-49660600	Active TSS	HepG2	liver
35	chr12:49659600-49661000	Enhancers	Spleen	Spleen
36	chr12:49659600-49661600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:49659600-49661800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
38	chr12:49659600-49662000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:49659600-49663200	Weak transcription	Fetal Brain Female	brain
40	chr12:49659600-49663400	Weak transcription	Ovary	ovary
41	chr12:49659600-49663800	Weak transcription	Brain Germinal Matrix	brain
42	chr12:49659600-49664800	Weak transcription	Fetal Lung	lung
43	chr12:49659600-49668600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:49659600-49669600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:49659600-49673600	Weak transcription	Brain Hippocampus Middle	brain
46	chr12:49659800-49660600	Enhancers	Primary B cells from peripheral blood	blood
47	chr12:49659800-49660600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr12:49659800-49660800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr12:49659800-49660800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:49659800-49660800	Enhancers	Fetal Muscle Trunk	muscle

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