Variant report

Variant	rs12310093
Chromosome Location	chr12:49660989-49660990
allele	A/C/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	HNF4G	chr12:49660975-49661292	HepG2	liver:	n/a	chr12:49661136-49661144 chr12:49661135-49661143 chr12:49661129-49661144 chr12:49661127-49661142 chr12:49661129-49661144
2	POLR2A	chr12:49658068-49661661	K562	blood:	n/a	n/a
3	POLR2A	chr12:49660345-49661089	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr12:49658351-49664605	U87	brain:	n/a	n/a
5	POLR2A	chr12:49658117-49661692	IMR90	lung:	n/a	n/a
6	POLR2A	chr12:49658070-49661060	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:49660160-49662050	K562	blood:	n/a	n/a
8	POLR2A	chr12:49658001-49664653	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr12:49657862-49669371	K562	blood:	n/a	n/a
10	POLR2A	chr12:49658069-49662113	K562	blood:	n/a	n/a
11	MAX	chr12:49660622-49661250	A549	lung:	n/a	chr12:49660890-49660899 chr12:49660890-49660899 chr12:49660890-49660899 chr12:49660889-49660900 chr12:49660889-49660900 chr12:49660890-49660900
12	POLR2A	chr12:49660080-49661193	PANC-1	pancreas:	n/a	n/a
13	NFIC	chr12:49660819-49661166	HepG2	liver:	n/a	n/a
14	EP300	chr12:49660929-49661569	HepG2	liver:	n/a	chr12:49661431-49661445 chr12:49661146-49661156
15	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
16	POLR2A	chr12:49660207-49662000	K562	blood:	n/a	n/a
17	POLR2A	chr12:49660073-49661228	HCT-116	colon:	n/a	n/a
18	MXI1	chr12:49660715-49661058	Hela-S3	cervix:	n/a	chr12:49660891-49660900 chr12:49660891-49660900
19	RCOR1	chr12:49660918-49661317	K562	blood:	n/a	n/a
20	MAX	chr12:49660706-49661020	K562	blood:	n/a	chr12:49660890-49660899 chr12:49660890-49660899 chr12:49660890-49660899 chr12:49660889-49660900 chr12:49660889-49660900 chr12:49660890-49660900
21	POLR2A	chr12:49660119-49662037	K562	blood:	n/a	n/a
22	POLR2A	chr12:49660194-49661761	Hela-S3	cervix:	n/a	n/a
23	TBL1XR1	chr12:49660817-49661145	K562	blood:	n/a	n/a
24	POLR2A	chr12:49660708-49661146	MCF-7	breast:	n/a	n/a
25	USF2	chr12:49660741-49661044	Hela-S3	cervix:	n/a	chr12:49660889-49660900
26	JUND	chr12:49660687-49661546	K562	blood:	n/a	chr12:49660760-49660774
27	FOXA1	chr12:49660897-49661594	HepG2	liver:	n/a	n/a
28	FOXA1	chr12:49660834-49661704	HepG2	liver:	n/a	n/a
29	POLR2A	chr12:49657881-49662104	U87	brain:	n/a	n/a
30	POLR2A	chr12:49657892-49662191	SK-N-MC	brain:	n/a	n/a
31	FOXA2	chr12:49660954-49661216	HepG2	liver:	n/a	n/a
32	FOXA1	chr12:49660845-49661648	HepG2	liver:	n/a	n/a
33	HEY1	chr12:49660069-49662204	K562	blood:	n/a	n/a
34	FOXA1	chr12:49660988-49661553	HepG2	liver:	n/a	n/a
35	POLR2A	chr12:49660147-49662192	GM12878	blood:	n/a	n/a
36	SIN3AK20	chr12:49660730-49661230	K562	blood:	n/a	n/a
37	POLR2A	chr12:49657998-49661215	HUVEC	blood vessel:	n/a	n/a
38	HCFC1	chr12:49657918-49661243	Hela-S3	cervix:	n/a	n/a
39	CEBPD	chr12:49660837-49661257	K562	blood:	n/a	n/a
40	POLR2A	chr12:49658323-49670206	PFSK-1	brain:	n/a	n/a
41	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
42	POLR2A	chr12:49660684-49661227	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr12:49660062-49661153	U87	brain:	n/a	n/a
44	POLR2A	chr12:49658134-49662185	GM12878	blood:	n/a	n/a
45	POLR2A	chr12:49660233-49661219	HUVEC	blood vessel:	n/a	n/a
46	FOXA2	chr12:49660894-49661595	A549	lung:	n/a	n/a
47	POLR2A	chr12:49658512-49661970	K562	blood:	n/a	n/a
48	POLR2A	chr12:49660973-49661754	GM12892	blood:	n/a	n/a
49	POLR2A	chr12:49660140-49661968	K562	blood:	n/a	n/a
50	FOXA2	chr12:49660804-49661602	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49656742..49663815-chr12:49736558..49745017,19	MCF-7	breast:
2	chr12:49523107..49527860-chr12:49656151..49664210,14	MCF-7	breast:
3	chr12:49519590..49527322-chr12:49655772..49662610,57	K562	blood:
4	chr12:49660606..49662503-chr12:62995463..62997195,2	MCF-7	breast:
5	chr12:49659293..49661080-chr22:50961474..50964056,2	K562	blood:
6	chr12:49448896..49462070-chr12:49656751..49663992,28	K562	blood:
7	chr12:49519914..49528393-chr12:49656527..49662615,75	K562	blood:
8	chr12:49446124..49447679-chr12:49658939..49661024,2	K562	blood:
9	chr12:49490563..49493344-chr12:49659510..49661117,2	K562	blood:
10	chr12:49499760..49506124-chr12:49657415..49661017,8	K562	blood:
11	chr12:49462406..49465445-chr12:49657502..49661212,4	K562	blood:
12	chr12:49207714..49211177-chr12:49657864..49661147,3	K562	blood:
13	chr12:49628076..49629914-chr12:49660607..49662737,2	MCF-7	breast:
14	chr12:49619902..49623805-chr12:49655877..49662372,6	K562	blood:
15	chr12:49449335..49458365-chr12:49656751..49666981,25	K562	blood:
16	chr12:49658775..49661727-chr12:49715622..49718429,2	K562	blood:
17	chr12:49657190..49661099-chr12:49688432..49694179,9	K562	blood:
18	chr12:49659146..49661010-chr12:49813234..49815442,2	K562	blood:
19	chr12:49660927..49665723-chr12:49685096..49688729,4	MCF-7	breast:
20	chr12:49656837..49661590-chr12:49759665..49765017,7	K562	blood:
21	chr12:49658339..49661093-chr12:49961458..49963113,2	MCF-7	breast:
22	chr12:49659194..49661044-chr17:57925096..57927054,2	MCF-7	breast:
23	chr12:49410141..49415550-chr12:49657481..49661686,9	K562	blood:
24	chr12:49580809..49583875-chr12:49657471..49661424,5	K562	blood:
25	chr12:49658135..49661109-chr12:50235815..50238160,2	MCF-7	breast:
26	chr12:49656722..49663896-chr12:49682381..49687774,8	K562	blood:
27	chr12:49522979..49526796-chr12:49655970..49661455,13	MCF-7	breast:
28	chr12:49657571..49662873-chr12:49757027..49762131,10	K562	blood:
29	chr12:49657208..49661363-chr12:49714955..49717990,5	MCF-7	breast:
30	chr12:49595504..49598364-chr12:49659060..49661146,3	K562	blood:
31	chr12:49452850..49457008-chr12:49658832..49661007,5	MCF-7	breast:
32	chr12:49656956..49663896-chr12:49681239..49693031,16	K562	blood:
33	chr12:49500184..49504763-chr12:49658087..49663330,8	K562	blood:
34	chr12:49655321..49661148-chr12:49729487..49743115,26	K562	blood:
35	chr12:49659282..49661011-chr12:49719290..49721807,2	K562	blood:
36	chr12:49657182..49662198-chr12:49738070..49742868,13	MCF-7	breast:
37	chr12:49580754..49584871-chr12:49657957..49661825,4	MCF-7	breast:
38	chr12:49397350..49399789-chr12:49659936..49661845,2	K562	blood:
39	chr12:49656941..49662685-chr12:49687034..49693573,13	MCF-7	breast:
40	chr12:49659208..49661762-chr12:49723498..49725947,3	K562	blood:
41	chr12:49483859..49489908-chr12:49657302..49662649,9	K562	blood:

Variant related genes	Relation type
ENSG00000258101	TF binding region
TUBA1C	TF binding region
ENSG00000186897	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000178401	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000139549	Chromatin interaction
ENSG00000130489	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000257354	Chromatin interaction
ENSG00000167552	Chromatin interaction
ENSG00000167550	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000272821	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000257346	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11168938	0.89[AFR][1000 genomes]
rs11168939	0.89[AFR][1000 genomes]
rs11168940	0.89[AFR][1000 genomes]
rs11168942	0.89[AFR][1000 genomes]
rs11168952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168953	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168955	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168956	0.92[AFR][1000 genomes]
rs11168957	0.92[AFR][1000 genomes]
rs11168958	0.92[AFR][1000 genomes]
rs11542115	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304483	0.86[AFR][1000 genomes]
rs12308571	0.92[AFR][1000 genomes]
rs17849881	0.85[EUR][1000 genomes]
rs17849882	0.85[EUR][1000 genomes]
rs28365885	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58403142	0.81[EUR][1000 genomes]
rs59965487	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62636517	0.81[EUR][1000 genomes]
rs62636520	0.81[EUR][1000 genomes]
rs73306246	1.00[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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49657600-49661000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr12:49657600-49661000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr12:49658000-49661400	Active TSS	HSMMtube	muscle
4	chr12:49658000-49661600	Active TSS	Esophagus	oesophagus
5	chr12:49659000-49663200	Transcr. at gene 5' and 3'	A549	lung
6	chr12:49659200-49673600	Weak transcription	Fetal Brain Male	brain
7	chr12:49659400-49661800	Weak transcription	Brain Substantia Nigra	brain
8	chr12:49659400-49664200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:49659600-49661000	Enhancers	Spleen	Spleen
10	chr12:49659600-49661600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:49659600-49661800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
12	chr12:49659600-49662000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:49659600-49663200	Weak transcription	Fetal Brain Female	brain
14	chr12:49659600-49663400	Weak transcription	Ovary	ovary
15	chr12:49659600-49663800	Weak transcription	Brain Germinal Matrix	brain
16	chr12:49659600-49664800	Weak transcription	Fetal Lung	lung
17	chr12:49659600-49668600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:49659600-49669600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:49659600-49673600	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:49659800-49661000	Enhancers	Primary hematopoietic stem cells	blood
21	chr12:49659800-49661000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr12:49659800-49661000	ZNF genes & repeats	Fetal Intestine Small	intestine
23	chr12:49659800-49661200	Weak transcription	Left Ventricle	heart
24	chr12:49659800-49661400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:49659800-49661600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:49659800-49661600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr12:49659800-49661600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:49659800-49661600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:49659800-49661600	Enhancers	Fetal Heart	heart
30	chr12:49659800-49662000	Transcr. at gene 5' and 3'	HMEC	breast
31	chr12:49659800-49662200	Weak transcription	Primary T cells from cord blood	blood
32	chr12:49659800-49662200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:49659800-49662200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:49659800-49662400	Weak transcription	Brain Anterior Caudate	brain
35	chr12:49659800-49662600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:49659800-49662600	Weak transcription	Fetal Kidney	kidney
37	chr12:49659800-49663000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr12:49659800-49663200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:49659800-49663600	Weak transcription	Primary B cells from cord blood	blood
40	chr12:49659800-49663600	Weak transcription	Aorta	Aorta
41	chr12:49659800-49663600	Weak transcription	Colon Smooth Muscle	Colon
42	chr12:49659800-49663800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr12:49659800-49668600	Weak transcription	Right Atrium	heart
44	chr12:49660000-49661000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:49660000-49661000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr12:49660000-49661000	ZNF genes & repeats	Fetal Intestine Large	intestine
47	chr12:49660000-49661400	Enhancers	Primary T cells fromperipheralblood	blood
48	chr12:49660000-49661400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:49660000-49661600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:49660000-49661600	Enhancers	Pancreas	Pancrea

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