Variant report

Variant	rs1544424
Chromosome Location	chr12:1098614-1098615
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	chr12:1098467-1101358	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr12:1098118-1098725	SH-SY5Y	brain:	n/a	chr12:1098694-1098704
3	POLR2A	chr12:1098580-1100894	PFSK-1	brain:	n/a	n/a
4	MXI1	chr12:1098181-1102272	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr12:1098283-1102022	MCF10A-Er-Src	breast:	n/a	n/a
6	CHD1	chr12:1098198-1102295	IMR90	lung:	n/a	chr12:1100770-1100780 chr12:1100805-1100815

No.	Distal block	Cell Line	Cell type
1	chr12:541135..544043-chr12:1097640..1100614,2	K562	blood:
2	chr12:1098483..1100095-chr12:1136049..1138258,2	K562	blood:
3	chr12:1058754..1060950-chr12:1097741..1100141,2	MCF-7	breast:
4	chr12:1082208..1083932-chr12:1096417..1099050,2	MCF-7	breast:
5	chr12:1056985..1060702-chr12:1098122..1101434,9	MCF-7	breast:
6	chr12:1097166..1102781-chr12:1103327..1109862,10	MCF-7	breast:

Variant related genes	Relation type
ERC1	TF binding region
ENSG00000120647	Chromatin interaction
ENSG00000082805	Chromatin interaction
ENSG00000002016	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10773922	1.00[AMR][1000 genomes]
rs10773923	1.00[AMR][1000 genomes]
rs10849618	0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2097859	0.81[YRI][hapmap]
rs2097860	1.00[AMR][1000 genomes]
rs2369494	1.00[AMR][1000 genomes]
rs4604948	1.00[AMR][1000 genomes]
rs4765691	1.00[AMR][1000 genomes]
rs4765901	0.87[AFR][1000 genomes]
rs4765965	0.87[YRI][hapmap]
rs61917250	0.95[AFR][1000 genomes]
rs6489778	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7311276	0.85[YRI][hapmap]
rs7972852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7974198	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv556890	chr12:662448-1100555	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS 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	58 gene(s)	inside rSNPs	diseases
5	nsv556892	chr12:673515-1210884	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	nsv948760	chr12:863833-1542875	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv1052589	chr12:910460-1421493	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1045278	chr12:920251-1697030	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
10	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
11	nsv468960	chr12:975276-1455106	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv556941	chr12:975276-1455106	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	nsv1044329	chr12:985144-1403020	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
14	nsv541340	chr12:985144-1403020	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv470256	chr12:998365-1438761	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	nsv492321	chr12:1011692-1388512	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
17	nsv898579	chr12:1013176-1510505	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv898580	chr12:1024688-1569097	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
19	nsv1036488	chr12:1041097-1445923	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
20	nsv1037825	chr12:1045734-1432940	Bivalent/Poised TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
21	nsv541342	chr12:1045734-1432940	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
22	nsv868854	chr12:1045935-1354083	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
23	nsv468962	chr12:1047531-1119958	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
24	nsv556942	chr12:1047531-1119958	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
25	esv2762958	chr12:1049279-1554962	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
26	nsv1052559	chr12:1077964-1588543	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
27	nsv898581	chr12:1084783-1527359	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
28	nsv1041799	chr12:1091294-1304839	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
29	nsv541343	chr12:1091294-1304839	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1073200-1099600	Weak transcription	Gastric	stomach
2	chr12:1078000-1099000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:1081600-1099600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:1082600-1099000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:1093400-1098800	Weak transcription	Right Ventricle	heart
6	chr12:1093600-1099000	Weak transcription	Placenta	Placenta
7	chr12:1096200-1099000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr12:1097200-1098800	Enhancers	Primary T cells from cord blood	blood
9	chr12:1097200-1098800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr12:1097200-1098800	Enhancers	Fetal Stomach	stomach
11	chr12:1097200-1098800	Enhancers	Thymus	Thymus
12	chr12:1097200-1099000	Enhancers	Primary hematopoietic stem cells	blood
13	chr12:1097200-1099200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:1097200-1099400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:1097400-1099400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:1097600-1098800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:1097600-1098800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr12:1097600-1098800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr12:1097600-1098800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:1097600-1098800	Enhancers	Fetal Intestine Large	intestine
21	chr12:1097600-1098800	Enhancers	Fetal Intestine Small	intestine
22	chr12:1097600-1098800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr12:1097600-1098800	Enhancers	HSMMtube	muscle
24	chr12:1097600-1099000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:1097600-1099000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr12:1097600-1099000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr12:1097600-1099000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr12:1097600-1099000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr12:1097600-1099000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:1097600-1099000	Enhancers	Fetal Thymus	thymus
31	chr12:1097600-1099200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:1097600-1099400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:1097600-1099400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:1097600-1099800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:1097600-1099800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:1097800-1098800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr12:1097800-1098800	Weak transcription	Brain Substantia Nigra	brain
38	chr12:1097800-1098800	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr12:1097800-1098800	Enhancers	HSMM	muscle
40	chr12:1097800-1098800	Enhancers	HUVEC	blood vessel
41	chr12:1097800-1098800	Enhancers	NH-A	brain
42	chr12:1097800-1099000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:1097800-1099000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:1097800-1099000	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr12:1097800-1099000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr12:1097800-1099000	Enhancers	Pancreas	Pancrea
47	chr12:1097800-1099000	Enhancers	Stomach Mucosa	stomach
48	chr12:1097800-1099000	Flanking Active TSS	NHLF	lung
49	chr12:1097800-1099200	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr12:1097800-1099200	Flanking Active TSS	Colon Smooth Muscle	Colon

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