Variant report

Variant	rs61546241
Chromosome Location	chr12:123463999-123464000
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123462700-123467376	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:123458534-123466263	K562	blood:	n/a	n/a
3	POLR2A	chr12:123462020-123470019	SK-N-MC	brain:	n/a	n/a
4	CTCF	chr12:123463940-123464090	SAEC	small airway:	n/a	n/a
5	BCL3	chr12:123463944-123465539	A549	lung:	n/a	n/a
6	POLR2A	chr12:123463966-123465607	GM12891	blood:	n/a	n/a
7	TCF12	chr12:123463846-123466004	A549	lung:	n/a	n/a
8	POLR2A	chr12:123463929-123465785	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:123463985-123466171	U87	brain:	n/a	n/a
10	POLR2A	chr12:123463935-123465551	K562	blood:	n/a	n/a
11	POLR2A	chr12:123463863-123469964	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr12:123460287-123466106	K562	blood:	n/a	n/a
13	POLR2A	chr12:123463987-123465698	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr12:123463967-123465853	GM12891	blood:	n/a	n/a
15	POLR2A	chr12:123463926-123464120	HCT-116	colon:	n/a	n/a
16	POLR2A	chr12:123463573-123466152	GM12892	blood:	n/a	n/a
17	POLR2A	chr12:123463985-123466477	U87	brain:	n/a	n/a
18	POLR2A	chr12:123463540-123464004	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:123462777-123467143	HL-60	blood:	n/a	n/a
20	POLR2A	chr12:123463131-123465669	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr12:123462997-123465931	HL-60	blood:	n/a	n/a
22	POLR2A	chr12:123463892-123465770	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:123463382-123465907	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr12:123463996-123465622	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr12:123463577-123466137	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:123463395-123466020	GM12892	blood:	n/a	n/a
27	ELF1	chr12:123463954-123466088	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:123463840-123464418	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr12:123463178-123465793	K562	blood:	n/a	n/a
30	POLR2A	chr12:123463126-123466154	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:123463370-123466657	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr12:123463562-123466014	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr12:123462975-123465829	K562	blood:	n/a	n/a
34	POLR2A	chr12:123462643-123465852	K562	blood:	n/a	n/a
35	POLR2A	chr12:123461706-123470094	K562	blood:	n/a	n/a
36	POLR2A	chr12:123463887-123465622	HepG2	liver:	n/a	n/a
37	POLR2A	chr12:123462922-123464544	A549	lung:	n/a	n/a
38	POLR2A	chr12:123462647-123470505	Hela-S3	cervix:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123374002..123376738-chr12:123462505..123465359,2	MCF-7	breast:
2	chr12:123463846..123466792-chr12:123754381..123757110,2	MCF-7	breast:
3	chr12:123463020..123465729-chr8:144897399..144899453,2	MCF-7	breast:
4	chr12:123463900..123467066-chr12:123633750..123636695,4	K562	blood:
5	chr12:123462407..123464564-chr12:123506369..123507907,2	MCF-7	breast:
6	chr12:123463187..123465154-chr12:123754619..123756805,2	K562	blood:
7	chr12:123463900..123466022-chr12:123633750..123636695,4	K562	blood:
8	chr12:123009242..123011639-chr12:123463173..123465225,2	K562	blood:
9	chr12:123317692..123320507-chr12:123463597..123466562,3	MCF-7	breast:
10	chr12:123345343..123346928-chr12:123463907..123466458,2	MCF-7	breast:
11	chr12:123463210..123468211-chr12:123716151..123721062,7	MCF-7	breast:
12	chr12:123463143..123466030-chr12:123559790..123563075,3	MCF-7	breast:
13	chr12:123318837..123320791-chr12:123463752..123466824,3	MCF-7	breast:

No data

Variant related genes	Relation type
ARL6IP4	TF binding region
ABCB9	TF binding region
ENSG00000139722	Chromatin interaction
ENSG00000090975	Chromatin interaction
ENSG00000180900	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000111011	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000111328	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10219462	0.89[AFR][1000 genomes]
rs11060932	0.88[AFR][1000 genomes]
rs11060997	0.89[AFR][1000 genomes]
rs11060999	0.89[AFR][1000 genomes]
rs11061578	0.86[AFR][1000 genomes]
rs12229884	0.89[AFR][1000 genomes]
rs12311043	0.89[AFR][1000 genomes]
rs34010146	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55646110	1.00[AMR][1000 genomes]
rs55796417	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55813219	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55830208	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55939945	1.00[AMR][1000 genomes]
rs55951195	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56020503	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56140750	0.83[AFR][1000 genomes]
rs56150478	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56288804	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56725866	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57106451	0.86[AFR][1000 genomes]
rs57110420	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57258703	1.00[AMR][1000 genomes]
rs57310784	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57641050	0.86[AFR][1000 genomes]
rs57764857	0.86[AFR][1000 genomes]
rs57794792	0.86[AFR][1000 genomes]
rs57863319	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58025094	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58462666	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59002329	0.85[AFR][1000 genomes]
rs59081274	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59211448	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59379557	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59526938	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60341839	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60341983	0.83[AFR][1000 genomes]
rs60358140	0.86[AFR][1000 genomes]
rs60739634	1.00[AMR][1000 genomes]
rs60809882	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60888713	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60920158	0.85[AMR][1000 genomes]
rs60987910	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61061591	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61377358	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61516893	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61592192	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61677786	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7295258	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406966	0.85[AMR][1000 genomes]
rs73406997	0.85[AMR][1000 genomes]
rs73408803	0.85[AMR][1000 genomes]
rs73408810	0.85[AMR][1000 genomes]
rs73408812	0.85[AMR][1000 genomes]
rs73408818	1.00[AMR][1000 genomes]
rs73408820	1.00[AMR][1000 genomes]
rs73408832	1.00[AMR][1000 genomes]
rs73408835	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408838	0.85[AMR][1000 genomes]
rs73408846	0.85[AMR][1000 genomes]
rs73408862	0.85[AFR][1000 genomes]
rs73408863	0.85[AFR][1000 genomes]
rs73408887	0.85[AMR][1000 genomes]
rs73408890	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408892	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408893	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408894	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408899	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411006	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411009	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411011	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411014	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411015	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411017	0.85[AMR][1000 genomes]
rs73411018	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411027	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411033	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411041	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411043	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411057	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411058	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411063	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411076	0.86[AFR][1000 genomes]
rs73411087	0.83[AFR][1000 genomes]
rs752164	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7952760	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv899577	chr12:123435248-123484474	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	nsv899578	chr12:123459005-123474529	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123460600-123464600	Weak transcription	Aorta	Aorta
2	chr12:123460800-123464000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:123460800-123464000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:123460800-123464600	Genic enhancers	Spleen	Spleen
5	chr12:123461000-123464000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:123461000-123464000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:123461000-123464000	Weak transcription	Fetal Heart	heart
8	chr12:123461000-123464000	Genic enhancers	Fetal Muscle Trunk	muscle
9	chr12:123461000-123464000	Weak transcription	HUVEC	blood vessel
10	chr12:123461000-123464200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:123461000-123464200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:123461000-123464200	Weak transcription	Fetal Kidney	kidney
13	chr12:123461000-123464200	Genic enhancers	Fetal Stomach	stomach
14	chr12:123461000-123464200	Genic enhancers	Fetal Thymus	thymus
15	chr12:123461000-123464400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:123461000-123464400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:123461200-123464000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:123461200-123464000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr12:123461200-123464000	Genic enhancers	Fetal Muscle Leg	muscle
20	chr12:123461400-123464000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:123461400-123464000	Weak transcription	Right Atrium	heart
22	chr12:123461400-123464200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:123461400-123464200	Weak transcription	Hela-S3	cervix
24	chr12:123461400-123473200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:123461600-123464000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:123461600-123464000	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr12:123461600-123464000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr12:123461600-123464000	Weak transcription	Esophagus	oesophagus
29	chr12:123461600-123464000	Weak transcription	Psoas Muscle	Psoas
30	chr12:123461800-123464000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr12:123462000-123464000	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:123462200-123464000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:123462400-123464000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:123462400-123464000	Weak transcription	K562	blood
35	chr12:123462600-123464000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:123462800-123464000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:123462800-123464200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:123463000-123464000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr12:123463000-123464000	Transcr. at gene 5' and 3'	Dnd41	blood
40	chr12:123463000-123464200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:123463000-123464600	Enhancers	Liver	Liver
42	chr12:123463200-123464000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
43	chr12:123463200-123464000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr12:123463200-123464000	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr12:123463200-123464000	Weak transcription	NHEK	skin
46	chr12:123463200-123464200	Enhancers	Primary T cells fromperipheralblood	blood
47	chr12:123463200-123464200	Enhancers	Primary hematopoietic stem cells	blood
48	chr12:123463200-123464200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr12:123463400-123464000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:123463400-123464000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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