Variant report

Variant	rs12308571
Chromosome Location	chr12:49660496-49660497
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	POLR2A	chr12:49658109-49660531	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:49660211-49660658	GM12892	blood:	n/a	n/a
3	POLR2A	chr12:49658068-49661661	K562	blood:	n/a	n/a
4	POLR2A	chr12:49660345-49661089	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr12:49660199-49660635	HCT-116	colon:	n/a	n/a
6	POLR2A	chr12:49658351-49664605	U87	brain:	n/a	n/a
7	POLR2A	chr12:49660155-49660702	HL-60	blood:	n/a	n/a
8	POLR2A	chr12:49660229-49660702	MCF-7	breast:	n/a	n/a
9	POLR2A	chr12:49658117-49661692	IMR90	lung:	n/a	n/a
10	POLR2A	chr12:49658070-49661060	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:49660160-49662050	K562	blood:	n/a	n/a
12	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
13	POLR2A	chr12:49658001-49664653	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr12:49657862-49669371	K562	blood:	n/a	n/a
15	POLR2A	chr12:49660311-49660601	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:49658069-49662113	K562	blood:	n/a	n/a
17	POLR2A	chr12:49660080-49661193	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr12:49660290-49660616	ECC-1	luminal epithelium:	n/a	n/a
19	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
20	POLR2A	chr12:49660207-49662000	K562	blood:	n/a	n/a
21	POLR2A	chr12:49660073-49661228	HCT-116	colon:	n/a	n/a
22	POLR2A	chr12:49660484-49660531	MCF-7	breast:	n/a	n/a
23	ZNF263	chr12:49660216-49660611	HEK293-T-REx	kidney:	n/a	n/a
24	POLR2A	chr12:49660119-49662037	K562	blood:	n/a	n/a
25	POLR2A	chr12:49660194-49661761	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr12:49658159-49660776	HepG2	liver:	n/a	n/a
27	POLR2A	chr12:49660363-49660605	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr12:49657881-49662104	U87	brain:	n/a	n/a
29	POLR2A	chr12:49657892-49662191	SK-N-MC	brain:	n/a	n/a
30	HEY1	chr12:49660069-49662204	K562	blood:	n/a	n/a
31	POLR2A	chr12:49658259-49660512	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr12:49660147-49662192	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:49657998-49661215	HUVEC	blood vessel:	n/a	n/a
34	HCFC1	chr12:49657918-49661243	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr12:49660280-49660622	GM12878	blood:	n/a	n/a
36	POLR2A	chr12:49658323-49670206	PFSK-1	brain:	n/a	n/a
37	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
38	POLR2A	chr12:49660062-49661153	U87	brain:	n/a	n/a
39	POLR2A	chr12:49658134-49662185	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:49660338-49660563	A549	lung:	n/a	n/a
41	POLR2A	chr12:49660311-49660601	A549	lung:	n/a	n/a
42	POLR2A	chr12:49660233-49661219	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr12:49658512-49661970	K562	blood:	n/a	n/a
44	POLR2A	chr12:49660140-49661968	K562	blood:	n/a	n/a
45	TCF7L2	chr12:49660338-49660620	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr12:49660135-49662199	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr12:49660084-49661224	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr12:49660217-49661800	HepG2	liver:	n/a	n/a
49	POLR2A	chr12:49658744-49662063	A549	lung:	n/a	n/a
50	HEY1	chr12:49660358-49661286	K562	blood:	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	chr12:49657320..49660807-chr12:49714613..49719662,6	K562	blood:
9	chr12:49487580..49490269-chr12:49658075..49660760,2	K562	blood:
10	chr12:49659293..49661080-chr22:50961474..50964056,2	K562	blood:
11	chr12:49448896..49462070-chr12:49656751..49663992,28	K562	blood:
12	chr12:49483859..49487327-chr12:49657616..49660606,5	K562	blood:
13	chr12:49519914..49528393-chr12:49656527..49662615,75	K562	blood:
14	chr12:49446124..49447679-chr12:49658939..49661024,2	K562	blood:
15	chr12:49501897..49506471-chr12:49657604..49660787,6	MCF-7	breast:
16	chr12:49490563..49493344-chr12:49659510..49661117,2	K562	blood:
17	chr12:49499760..49506124-chr12:49657415..49661017,8	K562	blood:
18	chr12:49462406..49465445-chr12:49657502..49661212,4	K562	blood:
19	chr12:49658793..49660553-chr12:49719371..49721124,2	MCF-7	breast:
20	chr12:49207714..49211177-chr12:49657864..49661147,3	K562	blood:
21	chr12:49630703..49633435-chr12:49659066..49660626,2	MCF-7	breast:
22	chr12:49657748..49660512-chr12:49730264..49732689,3	MCF-7	breast:
23	chr12:49657699..49660591-chr12:49932809..49935394,2	MCF-7	breast:
24	chr12:49619902..49623805-chr12:49655877..49662372,6	K562	blood:
25	chr12:49654800..49660850-chr12:49685742..49692441,19	MCF-7	breast:
26	chr12:49435486..49438666-chr12:49658667..49660787,3	MCF-7	breast:
27	chr12:49578543..49581092-chr12:49658927..49660844,2	K562	blood:
28	chr12:49449335..49458365-chr12:49656751..49666981,25	K562	blood:
29	chr12:49658775..49661727-chr12:49715622..49718429,2	K562	blood:
30	chr12:49657190..49661099-chr12:49688432..49694179,9	K562	blood:
31	chr12:49659146..49661010-chr12:49813234..49815442,2	K562	blood:
32	chr12:49658877..49660532-chr12:49934682..49936960,2	K562	blood:
33	chr12:49351320..49352963-chr12:49659062..49660649,2	K562	blood:
34	chr12:49656837..49661590-chr12:49759665..49765017,7	K562	blood:
35	chr12:49658339..49661093-chr12:49961458..49963113,2	MCF-7	breast:
36	chr12:49658305..49660610-chr22:29700972..29702617,2	K562	blood:
37	chr12:49659194..49661044-chr17:57925096..57927054,2	MCF-7	breast:
38	chr12:49410141..49415550-chr12:49657481..49661686,9	K562	blood:
39	chr12:49580809..49583875-chr12:49657471..49661424,5	K562	blood:
40	chr12:49658135..49661109-chr12:50235815..50238160,2	MCF-7	breast:
41	chr12:49656722..49663896-chr12:49682381..49687774,8	K562	blood:
42	chr12:49522979..49526796-chr12:49655970..49661455,13	MCF-7	breast:
43	chr12:49657571..49662873-chr12:49757027..49762131,10	K562	blood:
44	chr12:49657208..49661363-chr12:49714955..49717990,5	MCF-7	breast:
45	chr12:49434105..49439097-chr12:49658238..49660568,5	K562	blood:
46	chr12:49453115..49455291-chr12:49657846..49660975,4	MCF-7	breast:
47	chr12:49657502..49660502-chr12:50135111..50136880,4	K562	blood:
48	chr12:49581100..49585285-chr12:49656726..49660800,10	MCF-7	breast:
49	chr12:49595504..49598364-chr12:49659060..49661146,3	K562	blood:
50	chr12:49452850..49457008-chr12:49658832..49661007,5	MCF-7	breast:

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

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1109811	0.86[AFR][1000 genomes]
rs11168938	0.97[AFR][1000 genomes]
rs11168939	0.97[AFR][1000 genomes]
rs11168940	0.97[AFR][1000 genomes]
rs11168942	0.97[AFR][1000 genomes]
rs11168952	0.92[AFR][1000 genomes]
rs11168953	0.82[AFR][1000 genomes]
rs11168954	0.92[AFR][1000 genomes]
rs11168955	0.88[AFR][1000 genomes]
rs11168956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12304483	0.94[AFR][1000 genomes]
rs12309028	0.82[AFR][1000 genomes]
rs12310093	0.92[AFR][1000 genomes]
rs3759170	0.92[AFR][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	chr12:49657200-49660600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr12:49657600-49660600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:49657600-49660600	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr12:49657600-49661000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr12:49657600-49661000	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr12:49657800-49660600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr12:49657800-49660600	Active TSS	Hela-S3	cervix
8	chr12:49658000-49660800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:49658000-49660800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:49658000-49661400	Active TSS	HSMMtube	muscle
11	chr12:49658000-49661600	Active TSS	Esophagus	oesophagus
12	chr12:49659000-49663200	Transcr. at gene 5' and 3'	A549	lung
13	chr12:49659200-49673600	Weak transcription	Fetal Brain Male	brain
14	chr12:49659400-49661800	Weak transcription	Brain Substantia Nigra	brain
15	chr12:49659400-49664200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:49659600-49660600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:49659600-49660600	Active TSS	HepG2	liver
18	chr12:49659600-49661000	Enhancers	Spleen	Spleen
19	chr12:49659600-49661600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:49659600-49661800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
21	chr12:49659600-49662000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:49659600-49663200	Weak transcription	Fetal Brain Female	brain
23	chr12:49659600-49663400	Weak transcription	Ovary	ovary
24	chr12:49659600-49663800	Weak transcription	Brain Germinal Matrix	brain
25	chr12:49659600-49664800	Weak transcription	Fetal Lung	lung
26	chr12:49659600-49668600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:49659600-49669600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:49659600-49673600	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:49659800-49660600	Enhancers	Primary B cells from peripheral blood	blood
30	chr12:49659800-49660600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr12:49659800-49660800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr12:49659800-49660800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:49659800-49660800	Enhancers	Fetal Muscle Trunk	muscle
34	chr12:49659800-49660800	Weak transcription	Psoas Muscle	Psoas
35	chr12:49659800-49660800	Weak transcription	Right Ventricle	heart
36	chr12:49659800-49661000	Enhancers	Primary hematopoietic stem cells	blood
37	chr12:49659800-49661000	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr12:49659800-49661000	ZNF genes & repeats	Fetal Intestine Small	intestine
39	chr12:49659800-49661200	Weak transcription	Left Ventricle	heart
40	chr12:49659800-49661400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:49659800-49661600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:49659800-49661600	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr12:49659800-49661600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:49659800-49661600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:49659800-49661600	Enhancers	Fetal Heart	heart
46	chr12:49659800-49662000	Transcr. at gene 5' and 3'	HMEC	breast
47	chr12:49659800-49662200	Weak transcription	Primary T cells from cord blood	blood
48	chr12:49659800-49662200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:49659800-49662200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr12:49659800-49662400	Weak transcription	Brain Anterior Caudate	brain

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