Variant report

Variant	rs12740112
Chromosome Location	chr1:180940912-180940913
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	chr1:180940033-180940994	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:180940639-180941052	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:180938068..180941019-chr1:181056460..181059037,4	K562	blood:
2	chr1:180932996..180935455-chr1:180937795..180941673,3	MCF-7	breast:
3	chr1:180940141..180942876-chr1:180990476..180992121,2	MCF-7	breast:
4	chr1:180933034..180938105-chr1:180938834..180942220,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234237	TF binding region
ENSG00000135823	Chromatin interaction
ENSG00000162783	Chromatin interaction
ENSG00000251520	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10910851	0.81[ASN][1000 genomes]
rs10914146	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12036052	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12092435	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2183424	0.81[ASN][1000 genomes]
rs2331902	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs3789363	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12740112	GLUL	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180918600-180944800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:180922600-180949400	Strong transcription	Dnd41	blood
3	chr1:180923600-180944800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:180923600-180958800	Weak transcription	Small Intestine	intestine
5	chr1:180923800-180942800	Weak transcription	Fetal Lung	lung
6	chr1:180923800-180944800	Weak transcription	HUVEC	blood vessel
7	chr1:180923800-180944800	Weak transcription	NH-A	brain
8	chr1:180924000-180941600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:180924200-180941600	Weak transcription	Pancreas	Pancrea
10	chr1:180924200-180942000	Weak transcription	Liver	Liver
11	chr1:180924200-180943400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:180929000-180956200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:180930200-180950200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:180931600-180941800	Weak transcription	Placenta	Placenta
15	chr1:180931600-180950800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:180932000-180942600	Weak transcription	HSMMtube	muscle
17	chr1:180932000-180944800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:180932200-180941600	Weak transcription	Fetal Kidney	kidney
19	chr1:180932200-180942600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:180932800-180943000	Strong transcription	Fetal Stomach	stomach
21	chr1:180933200-180947200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:180933400-180948000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:180933400-180974600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:180933600-180943400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:180933800-180944200	Strong transcription	Primary T cells from cord blood	blood
26	chr1:180933800-180948800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:180934200-180943800	Strong transcription	Fetal Intestine Large	intestine
28	chr1:180936400-180941600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:180936600-180942400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:180936600-180944000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:180937200-180942400	Weak transcription	Fetal Heart	heart
32	chr1:180937600-180942200	Strong transcription	Fetal Intestine Small	intestine
33	chr1:180937600-180942400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:180937800-180943400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:180937800-180950200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:180937800-180950400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:180938000-180942200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:180938000-180942400	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:180938000-180943200	Strong transcription	Spleen	Spleen
40	chr1:180938000-180943400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:180938000-180943400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:180938000-180944200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:180938000-180947000	Strong transcription	Thymus	Thymus
44	chr1:180938200-180941800	Strong transcription	NHEK	skin
45	chr1:180938200-180943600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:180938200-180946600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:180938400-180941800	Strong transcription	Brain Germinal Matrix	brain
48	chr1:180938400-180942000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:180938400-180944000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr1:180938400-180944200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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