Variant report

Variant	rs28360475
Chromosome Location	chr12:121477046-121477047
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	TBP	chr12:121476634-121477242	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:121476549-121477181	HCT-116	colon:	n/a	n/a
3	USF2	chr12:121477031-121477201	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:121476579-121477252	HCT-116	colon:	n/a	n/a
5	STAT1	chr12:121476656-121477289	K562	blood:	n/a	chr12:121477056-121477067
6	POLR2A	chr12:121476079-121477334	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:121476403-121477315	GM12892	blood:	n/a	n/a
8	ZNF384	chr12:121476853-121477490	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:121476541-121477303	GM12878	blood:	n/a	n/a
10	GATA3	chr12:121476570-121477201	T-47D	breast:	n/a	n/a
11	POLR2A	chr12:121476541-121477297	GM19099	blood:	n/a	n/a
12	SPI1	chr12:121476886-121477237	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:121476397-121477125	U87	brain:	n/a	n/a
14	STAT2	chr12:121476303-121477299	K562	blood:	n/a	chr12:121477056-121477067 chr12:121477053-121477068
15	RUNX3	chr12:121476900-121477337	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:121476438-121477356	GM12892	blood:	n/a	n/a
17	RUNX3	chr12:121476568-121477255	GM12878	blood:	n/a	n/a
18	ATF2	chr12:121476753-121477249	GM12878	blood:	n/a	n/a
19	STAT3	chr12:121476821-121477180	MCF10A-Er-Src	breast:	n/a	chr12:121477056-121477067
20	IKZF1	chr12:121476511-121477327	GM12878	blood:	n/a	n/a
21	MYC	chr12:121476975-121477238	MCF10A-Er-Src	breast:	n/a	n/a
22	IRF1	chr12:121476631-121477262	K562	blood:	n/a	chr12:121477054-121477068 chr12:121477096-121477113 chr12:121477055-121477069 chr12:121477054-121477068 chr12:121477055-121477068
23	YY1	chr12:121476567-121477070	GM12892	blood:	n/a	n/a
24	YY1	chr12:121476863-121477084	GM12878	blood:	n/a	n/a
25	POLR2A	chr12:121476495-121477256	GM18526	blood:	n/a	n/a
26	EBF1	chr12:121476601-121477298	GM12878	blood:	n/a	n/a
27	MTA3	chr12:121476480-121477326	GM12878	blood:	n/a	n/a
28	ZNF143	chr12:121476711-121477104	GM12878	blood:	n/a	chr12:121476880-121476895
29	POU2F2	chr12:121476304-121477331	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:121476391-121477142	U87	brain:	n/a	n/a
31	POLR2A	chr12:121476480-121477321	GM12891	blood:	n/a	n/a
32	RELA	chr12:121476436-121477232	GM18951	blood:	n/a	n/a
33	POLR2A	chr12:121476545-121477148	GM15510	blood:	n/a	n/a
34	PAX5	chr12:121476576-121477079	GM12878	blood:	n/a	n/a
35	FOS	chr12:121476914-121477114	MCF10A-Er-Src	breast:	n/a	n/a
36	STAT3	chr12:121476808-121477248	MCF10A-Er-Src	breast:	n/a	chr12:121477056-121477067
37	SP1	chr12:121476372-121477369	HCT-116	colon:	n/a	chr12:121476548-121476562
38	PBX3	chr12:121476930-121477121	GM12878	blood:	n/a	n/a
39	SPI1	chr12:121476866-121477207	GM12891	blood:	n/a	n/a
40	WRNIP1	chr12:121476357-121477250	GM12878	blood:	n/a	n/a
41	STAT1	chr12:121476864-121477248	K562	blood:	n/a	chr12:121477056-121477067
42	ZNF263	chr12:121476547-121477162	HEK293-T-REx	kidney:	n/a	chr12:121476890-121476899
43	POLR2A	chr12:121476310-121477350	Hela-S3	cervix:	n/a	n/a
44	STAT3	chr12:121476706-121477201	MCF10A-Er-Src	breast:	n/a	chr12:121477056-121477067
45	STAT3	chr12:121476854-121477227	MCF10A-Er-Src	breast:	n/a	chr12:121477056-121477067
46	SP1	chr12:121476524-121477341	A549	lung:	n/a	chr12:121476548-121476562
47	TBP	chr12:121476434-121477292	GM12878	blood:	n/a	n/a
48	FOS	chr12:121476869-121477224	MCF10A-Er-Src	breast:	n/a	n/a
49	MYC	chr12:121476825-121477054	MCF10A-Er-Src	breast:	n/a	n/a
50	PAX5	chr12:121476497-121477050	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
OASL	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs34119995	0.82[ASN][1000 genomes]
rs73214160	0.82[ASN][1000 genomes]
rs73214166	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73214167	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73214168	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73214174	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73214176	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73214177	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73214178	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73214179	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73214180	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73214181	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73214182	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73214184	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73214185	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73214186	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73214187	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv1039216	chr12:121421701-121538491	Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	esv3421024	chr12:121471004-121493702	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121475600-121477400	Flanking Active TSS	GM12878-XiMat	blood
2	chr12:121475800-121477200	Active TSS	Stomach Mucosa	stomach
3	chr12:121476000-121477400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
4	chr12:121476000-121477400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:121476000-121477400	Active TSS	Rectal Smooth Muscle	rectum
6	chr12:121476000-121477400	Flanking Active TSS	Hela-S3	cervix
7	chr12:121476200-121477200	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr12:121476200-121477200	Active TSS	Colon Smooth Muscle	Colon
9	chr12:121476200-121477200	Flanking Active TSS	Fetal Thymus	thymus
10	chr12:121476200-121477200	Active TSS	Gastric	stomach
11	chr12:121476200-121477400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr12:121476200-121477400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:121476200-121477400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:121476200-121477400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:121476200-121477400	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr12:121476200-121477400	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr12:121476200-121477400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr12:121476200-121477400	Active TSS	Left Ventricle	heart
19	chr12:121476200-121477400	Active TSS	Thymus	Thymus
20	chr12:121476200-121477400	Flanking Active TSS	Dnd41	blood
21	chr12:121476200-121477400	Flanking Active TSS	NHEK	skin
22	chr12:121476400-121477200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:121476400-121477200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:121476400-121477200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:121476400-121477200	Flanking Active TSS	Placenta	Placenta
26	chr12:121476400-121477200	Flanking Active TSS	Ovary	ovary
27	chr12:121476400-121477200	Active TSS	Pancreas	Pancrea
28	chr12:121476400-121477200	Active TSS	Psoas Muscle	Psoas
29	chr12:121476400-121477200	Flanking Active TSS	Osteobl	bone
30	chr12:121476400-121477400	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr12:121476400-121477400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr12:121476400-121477400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:121476400-121477400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr12:121476400-121477400	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr12:121476400-121477400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
36	chr12:121476400-121477400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
37	chr12:121476600-121477200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
38	chr12:121476600-121477200	Bivalent/Poised TSS	Fetal Stomach	stomach
39	chr12:121476600-121477200	Active TSS	Small Intestine	intestine
40	chr12:121476600-121477200	Active TSS	Spleen	Spleen
41	chr12:121476600-121477200	Flanking Bivalent TSS/Enh	HepG2	liver
42	chr12:121476600-121477200	Bivalent/Poised TSS	NHLF	lung
43	chr12:121476600-121477400	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr12:121476600-121477400	Active TSS	Primary T cells from cord blood	blood
45	chr12:121476600-121477400	Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr12:121476600-121477400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:121476600-121477400	Active TSS	Fetal Kidney	kidney
48	chr12:121476800-121477200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:121476800-121477200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
50	chr12:121476800-121477200	Flanking Active TSS	Brain Anterior Caudate	brain

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