Variant report

Variant	rs1148554
Chromosome Location	chr12:57919107-57919108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57916882-57919110	U87	brain:	n/a	n/a
2	POLR2A	chr12:57911713-57919299	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr12:57908382-57921207	K562	blood:	n/a	n/a
4	POLR2A	chr12:57915375-57927219	K562	blood:	n/a	n/a
5	POLR2A	chr12:57912610-57921102	K562	blood:	n/a	n/a
6	POLR2A	chr12:57908062-57920927	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57918214..57920020-chr12:58015895..58018076,2	MCF-7	breast:
2	chr12:57850154..57858218-chr12:57910899..57919538,20	K562	blood:
3	chr12:57889487..57901620-chr12:57907600..57919310,30	K562	blood:
4	chr12:57856862..57858591-chr12:57918787..57921199,2	MCF-7	breast:

No data

Variant related genes	Relation type
MBD6	TF binding region
DDIT3	TF binding region
ENSG00000111087	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000135502	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1148553	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1148555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148557	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1284465	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1284605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1299737	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1629410	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1669294	0.88[EUR][1000 genomes]
rs1669296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669297	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678537	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1679368	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1709871	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1709874	0.86[EUR][1000 genomes]
rs2127318	1.00[CEU][hapmap];0.81[CHB][hapmap];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2620677	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2620679	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2672571	0.92[CEU][hapmap]
rs2928382	0.86[EUR][1000 genomes]
rs2943696	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782129	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3847699	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs474544	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760273	0.84[EUR][1000 genomes]
rs496245	0.92[CEU][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs508904	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs511752	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs542278	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs697221	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703835	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs703836	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs703837	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs703838	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs703839	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7299631	0.96[EUR][1000 genomes]
rs747340	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs775236	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775237	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775241	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs775323	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs775324	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs776038	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs776039	0.87[EUR][1000 genomes]
rs7964074	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs796546	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7969683	0.83[EUR][1000 genomes]
rs9737891	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer 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	89 gene(s)	inside rSNPs	diseases
8	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
9	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
10	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' 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	89 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	nsv899120	chr12:57886609-57921188	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers 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 miRNA target site	72 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57917200-57920800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:57917400-57922800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:57917600-57920400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:57917600-57921000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:57917600-57939600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:57917800-57919200	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr12:57917800-57919200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr12:57917800-57919400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:57917800-57919600	Genic enhancers	Left Ventricle	heart
10	chr12:57917800-57920200	Enhancers	Fetal Brain Male	brain
11	chr12:57917800-57920600	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr12:57917800-57920800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:57917800-57921400	Genic enhancers	Fetal Muscle Trunk	muscle
14	chr12:57917800-57922400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:57918000-57919200	Genic enhancers	Colon Smooth Muscle	Colon
16	chr12:57918000-57919200	Genic enhancers	Rectal Mucosa Donor 31	rectum
17	chr12:57918000-57919400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:57918000-57919400	Genic enhancers	Primary monocytes fromperipheralblood	blood
19	chr12:57918000-57919400	Genic enhancers	Fetal Stomach	stomach
20	chr12:57918000-57919400	Genic enhancers	Rectal Mucosa Donor 29	rectum
21	chr12:57918000-57919600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:57918000-57919800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:57918000-57919800	Genic enhancers	Right Ventricle	heart
24	chr12:57918000-57920000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:57918000-57920000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
26	chr12:57918000-57920200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:57918000-57920200	Genic enhancers	Fetal Brain Female	brain
28	chr12:57918000-57920400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:57918000-57921200	Genic enhancers	Fetal Muscle Leg	muscle
30	chr12:57918000-57924000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:57918200-57919400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:57918200-57919400	Genic enhancers	Brain Cingulate Gyrus	brain
33	chr12:57918200-57919600	Genic enhancers	Placenta	Placenta
34	chr12:57918200-57920200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:57918200-57920200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:57918200-57921000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:57918400-57919200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:57918400-57919200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
39	chr12:57918400-57919400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
40	chr12:57918400-57919400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
41	chr12:57918400-57919400	Genic enhancers	Monocytes-CD14+_RO01746	blood
42	chr12:57918400-57919600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr12:57918400-57919600	Genic enhancers	Stomach Mucosa	stomach
44	chr12:57918400-57920200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:57918400-57920200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
46	chr12:57918400-57920800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:57918400-57920800	Genic enhancers	Fetal Thymus	thymus
48	chr12:57918400-57921200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:57918400-57929400	Strong transcription	Ovary	ovary
50	chr12:57918400-57929800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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