Variant report

Variant	rs10744555
Chromosome Location	chr12:1949463-1949464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:1947284..1949728-chr12:2036486..2038838,2	MCF-7	breast:
2	chr12:1925102..1928805-chr12:1946979..1949915,3	MCF-7	breast:
3	chr12:1920587..1924096-chr12:1946145..1949569,4	MCF-7	breast:
4	chr12:1944160..1952960-chr12:2039965..2049915,22	MCF-7	breast:
5	chr12:1947774..1950374-chr12:1986873..1988503,2	MCF-7	breast:
6	chr12:1901985..1907754-chr12:1946580..1951659,8	MCF-7	breast:
7	chr12:1947643..1951345-chr12:1957413..1959557,3	MCF-7	breast:
8	chr12:1799987..1802012-chr12:1946925..1950411,3	MCF-7	breast:
9	chr12:1877224..1880546-chr12:1949279..1951143,3	MCF-7	breast:
10	chr12:1910081..1912246-chr12:1949040..1950547,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000151062	Chromatin interaction
ENSG00000006831	Chromatin interaction
ENSG00000235049	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10744554	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2041140	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2041141	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2108639	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2108641	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4765645	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4766424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7135189	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7138109	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs721159	0.88[EUR][1000 genomes]
rs7303599	0.84[EUR][1000 genomes]
rs7303742	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs758161	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs758165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7960850	0.92[AFR][1000 genomes]
rs886942	0.97[EUR][1000 genomes]
rs9971758	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv832306	chr12:1847726-2001308	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv430442	chr12:1889823-1982151	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv1824001	chr12:1896738-1951940	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv898593	chr12:1901485-1962759	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv518013	chr12:1914273-1952990	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv898594	chr12:1916838-1952990	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv898595	chr12:1916838-1962759	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv898596	chr12:1923040-1962759	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv898597	chr12:1928289-1962759	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv934103	chr12:1935388-1984604	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv898598	chr12:1939252-2215448	Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1050895	chr12:1941618-1983445	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	nsv898599	chr12:1942752-1989355	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
15	nsv1038109	chr12:1944485-1985227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
16	nsv1040260	chr12:1947193-1983782	Weak transcription Bivalent Enhancer Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv556999	chr12:1948947-1981450	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1940800-1953400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:1945200-1950600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:1945800-1950000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr12:1945800-1950600	Enhancers	Brain Germinal Matrix	brain
5	chr12:1946000-1949800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:1946000-1950400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:1946200-1951000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:1946600-1949800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:1946800-1952600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:1947200-1953400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:1947400-1950800	Enhancers	HepG2	liver
12	chr12:1948200-1950000	Enhancers	Fetal Brain Female	brain
13	chr12:1948600-1949600	Weak transcription	Spleen	Spleen
14	chr12:1948600-1954000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr12:1948800-1950200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr12:1948800-1950600	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr12:1949000-1949800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:1949000-1949800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:1949000-1949800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:1949000-1950000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:1949000-1952400	Enhancers	Primary B cells from cord blood	blood
22	chr12:1949000-1952800	Enhancers	Primary B cells from peripheral blood	blood
23	chr12:1949200-1949600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:1949200-1949600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr12:1949200-1949600	Weak transcription	Fetal Brain Male	brain
26	chr12:1949400-1951000	Weak transcription	Primary hematopoietic stem cells	blood

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