Variant report

Variant	rs73408899
Chromosome Location	chr12:123462262-123462263
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	ZNF263	chr12:123462111-123462515	HEK293-T-REx	kidney:	n/a	chr12:123462327-123462336 chr12:123462347-123462368
2	POLR2A	chr12:123462233-123462267	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr12:123458534-123466263	K562	blood:	n/a	n/a
4	POLR2A	chr12:123462020-123470019	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr12:123461868-123462304	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:123460287-123466106	K562	blood:	n/a	n/a
7	POLR2A	chr12:123461913-123462372	K562	blood:	n/a	n/a
8	POLR2A	chr12:123461706-123470094	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123459054..123462367-chr12:123715409..123720380,5	K562	blood:
2	chr12:123458147..123462549-chr12:123715608..123720287,8	MCF-7	breast:

Variant related genes	Relation type
ABCB9	TF binding region
ARL6IP4	TF binding region
ENSG00000051825	Chromatin interaction
ENSG00000130921	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	0.92[AFR][1000 genomes]
rs11060932	0.90[AFR][1000 genomes]
rs11060997	0.92[AFR][1000 genomes]
rs11060999	0.92[AFR][1000 genomes]
rs11061578	0.83[AFR][1000 genomes]
rs12229884	0.92[AFR][1000 genomes]
rs12311043	0.92[AFR][1000 genomes]
rs34010146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55646110	1.00[AMR][1000 genomes]
rs55796417	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55813219	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55830208	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55939945	1.00[AMR][1000 genomes]
rs55951195	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56020503	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56140750	0.81[AFR][1000 genomes]
rs56150478	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56288804	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56725866	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57106451	0.83[AFR][1000 genomes]
rs57110420	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57258703	1.00[AMR][1000 genomes]
rs57310784	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57641050	0.83[AFR][1000 genomes]
rs57764857	0.83[AFR][1000 genomes]
rs57794792	0.83[AFR][1000 genomes]
rs57863319	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58025094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58462666	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59002329	0.88[AFR][1000 genomes]
rs59081274	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59211448	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59379557	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59526938	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60341839	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60341983	0.81[AFR][1000 genomes]
rs60358140	0.83[AFR][1000 genomes]
rs60739634	1.00[AMR][1000 genomes]
rs60809882	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60888713	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60920158	0.85[AMR][1000 genomes]
rs60987910	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61061591	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61377358	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61516893	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61546241	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61592192	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61677786	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7295258	0.86[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	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408838	0.85[AMR][1000 genomes]
rs73408846	0.85[AMR][1000 genomes]
rs73408862	0.88[AFR][1000 genomes]
rs73408863	0.88[AFR][1000 genomes]
rs73408887	0.85[AMR][1000 genomes]
rs73408890	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408892	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408893	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408894	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411006	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411009	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411011	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411014	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411015	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411017	0.85[AMR][1000 genomes]
rs73411018	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411027	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411033	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411041	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411043	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411057	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411058	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411063	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411076	0.83[AFR][1000 genomes]
rs73411087	0.81[AFR][1000 genomes]
rs752164	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7952760	0.81[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	chr12:123460600-123462800	Enhancers	Fetal Brain Male	brain
2	chr12:123460600-123464600	Weak transcription	Aorta	Aorta
3	chr12:123460800-123464000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:123460800-123464000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:123460800-123464600	Genic enhancers	Spleen	Spleen
6	chr12:123461000-123463800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:123461000-123463800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:123461000-123463800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:123461000-123463800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr12:123461000-123463800	Weak transcription	Small Intestine	intestine
11	chr12:123461000-123464000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:123461000-123464000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:123461000-123464000	Weak transcription	Fetal Heart	heart
14	chr12:123461000-123464000	Genic enhancers	Fetal Muscle Trunk	muscle
15	chr12:123461000-123464000	Weak transcription	HUVEC	blood vessel
16	chr12:123461000-123464200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr12:123461000-123464200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:123461000-123464200	Weak transcription	Fetal Kidney	kidney
19	chr12:123461000-123464200	Genic enhancers	Fetal Stomach	stomach
20	chr12:123461000-123464200	Genic enhancers	Fetal Thymus	thymus
21	chr12:123461000-123464400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:123461000-123464400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:123461200-123462400	Enhancers	Brain Angular Gyrus	brain
24	chr12:123461200-123463200	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr12:123461200-123463400	Weak transcription	A549	lung
26	chr12:123461200-123463600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:123461200-123463600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr12:123461200-123463600	Genic enhancers	Lung	lung
29	chr12:123461200-123463600	Weak transcription	HSMM	muscle
30	chr12:123461200-123463800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:123461200-123463800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:123461200-123463800	Genic enhancers	Fetal Intestine Large	intestine
33	chr12:123461200-123463800	Genic enhancers	Fetal Intestine Small	intestine
34	chr12:123461200-123463800	Genic enhancers	Gastric	stomach
35	chr12:123461200-123463800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr12:123461200-123463800	Weak transcription	HSMMtube	muscle
37	chr12:123461200-123463800	Weak transcription	NH-A	brain
38	chr12:123461200-123464000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:123461200-123464000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr12:123461200-123464000	Genic enhancers	Fetal Muscle Leg	muscle
41	chr12:123461400-123462600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:123461400-123462800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:123461400-123462800	Enhancers	Adipose Nuclei	Adipose
44	chr12:123461400-123463000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr12:123461400-123463000	Genic enhancers	Liver	Liver
46	chr12:123461400-123463000	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr12:123461400-123463400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:123461400-123463400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:123461400-123463400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:123461400-123463600	Genic enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links