Variant report

Variant	rs3782129
Chromosome Location	chr12:57936939-57936940
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57935626..57940631-chr12:58026197..58030320,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DDIT3-2	chr12:57936730-57936965	NONHSAT028936

Variant related genes	Relation type
ENSG00000135454	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1148553	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1148554	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1148555	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1148557	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1284465	0.86[EUR][1000 genomes]
rs1284605	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1299737	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1629410	0.87[EUR][1000 genomes]
rs1669294	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1669296	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1669297	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1678537	0.84[EUR][1000 genomes]
rs1679368	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1709871	0.87[EUR][1000 genomes]
rs1709874	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2127318	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2620677	0.82[EUR][1000 genomes]
rs2620679	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2928382	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2943696	0.83[EUR][1000 genomes]
rs3847699	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs474544	0.84[EUR][1000 genomes]
rs4760273	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs496245	0.84[EUR][1000 genomes]
rs697221	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs703835	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs703836	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs703837	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs703838	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs703839	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7299631	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs747340	0.87[EUR][1000 genomes]
rs775236	0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs775237	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs775241	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775323	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs775324	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs776038	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs776039	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7964074	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs796546	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7969683	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9737891	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
2	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
8	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
9	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
10	nsv1053930	chr12:57921188-57969659	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57917600-57939600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:57918600-57939600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:57919000-57937400	Weak transcription	Right Atrium	heart
4	chr12:57919200-57939600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:57919400-57937800	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:57919400-57939400	Strong transcription	Fetal Stomach	stomach
7	chr12:57919800-57937000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:57919800-57937800	Strong transcription	Fetal Intestine Small	intestine
9	chr12:57920000-57937800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:57920200-57937400	Strong transcription	Fetal Brain Female	brain
11	chr12:57920400-57938600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:57920600-57938800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:57920800-57937000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:57920800-57937200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:57921000-57938800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:57921200-57938600	Strong transcription	Fetal Muscle Leg	muscle
17	chr12:57921400-57939600	Strong transcription	Fetal Muscle Trunk	muscle
18	chr12:57921800-57937400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:57923000-57939800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:57923400-57937800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:57924200-57937600	Strong transcription	Placenta	Placenta
22	chr12:57924400-57937400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:57927200-57937200	Weak transcription	Fetal Heart	heart
24	chr12:57927200-57939200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr12:57928400-57937200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:57928400-57937400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:57928400-57937600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr12:57928400-57939600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:57929000-57937600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:57929000-57939400	Weak transcription	Small Intestine	intestine
31	chr12:57929000-57939600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:57929400-57939200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr12:57929600-57939600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:57929600-57939600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:57929800-57937400	Weak transcription	Brain Anterior Caudate	brain
36	chr12:57931600-57939200	Strong transcription	A549	lung
37	chr12:57932600-57939600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:57932800-57939600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr12:57932800-57939600	Weak transcription	Psoas Muscle	Psoas
40	chr12:57933000-57937000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:57933200-57938600	Weak transcription	Fetal Brain Male	brain
42	chr12:57933200-57938600	Weak transcription	GM12878-XiMat	blood
43	chr12:57933200-57939800	Weak transcription	Fetal Kidney	kidney
44	chr12:57933400-57937200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr12:57933400-57937200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr12:57933400-57937200	Weak transcription	Pancreas	Pancrea
47	chr12:57933400-57937200	Weak transcription	HSMM	muscle
48	chr12:57933400-57938600	Weak transcription	Gastric	stomach
49	chr12:57933400-57939600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr12:57933400-57940000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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