Variant report

Variant	rs1901240
Chromosome Location	chr12:62791105-62791106
allele	C/T
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	chr12:62789020-62791368	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:62790233..62792343-chr12:62793733..62795768,2	MCF-7	breast:
2	chr12:62783680..62786866-chr12:62789094..62791660,3	K562	blood:
3	chr12:62788984..62792175-chr12:62792277..62796551,3	K562	blood:

Variant related genes	Relation type
USP15	TF binding region
ENSG00000135655	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10747960	0.91[ASN][1000 genomes]
rs10877839	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs11174451	0.85[ASN][1000 genomes]
rs11174452	0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs11174455	0.91[ASN][1000 genomes]
rs11174465	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11613953	0.88[MKK][hapmap]
rs11836392	0.88[ASN][1000 genomes]
rs12818222	0.90[ASN][1000 genomes]
rs1390853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1532435	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs17097891	0.88[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs17120331	0.81[ASN][1000 genomes]
rs17717132	0.88[MKK][hapmap]
rs4145153	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs57361004	0.87[ASN][1000 genomes]
rs767390	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053403	chr12:62657011-62809413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv899153	chr12:62716330-62817736	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1803510	chr12:62729782-62802643	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv469417	chr12:62751242-62802643	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv559155	chr12:62751242-62802643	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv899154	chr12:62764909-62811328	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv899155	chr12:62764909-62817736	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv899156	chr12:62783967-62831343	Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv899157	chr12:62783967-62843620	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv899158	chr12:62783967-62937259	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1901240	SHMT2	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62738800-62792800	Weak transcription	Lung	lung
2	chr12:62762400-62796600	Weak transcription	Fetal Brain Male	brain
3	chr12:62763000-62805400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr12:62764200-62792000	Weak transcription	HepG2	liver
5	chr12:62765800-62795000	Weak transcription	Small Intestine	intestine
6	chr12:62767400-62807600	Weak transcription	HSMMtube	muscle
7	chr12:62769200-62805000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr12:62769400-62797400	Weak transcription	Right Ventricle	heart
9	chr12:62769400-62809600	Weak transcription	Stomach Mucosa	stomach
10	chr12:62772600-62800800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:62773000-62792800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:62773200-62799400	Weak transcription	Brain Substantia Nigra	brain
13	chr12:62773600-62802400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:62774200-62800000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr12:62774200-62802200	Strong transcription	Dnd41	blood
16	chr12:62774400-62799400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:62774400-62802200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:62774600-62802000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr12:62774800-62801600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:62774800-62802200	Strong transcription	Fetal Thymus	thymus
21	chr12:62774800-62803200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:62775200-62802000	Strong transcription	Primary B cells from cord blood	blood
23	chr12:62775200-62802600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr12:62775600-62807800	Weak transcription	Aorta	Aorta
25	chr12:62776200-62795200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:62777000-62799400	Strong transcription	Liver	Liver
27	chr12:62777000-62801200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:62777200-62799600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:62777600-62792000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:62778600-62800400	Weak transcription	Psoas Muscle	Psoas
31	chr12:62779200-62794400	Strong transcription	Primary hematopoietic stem cells	blood
32	chr12:62780000-62791400	Weak transcription	Gastric	stomach
33	chr12:62781200-62801600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:62782200-62793600	Strong transcription	Primary B cells from peripheral blood	blood
35	chr12:62782200-62799200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:62782200-62799400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr12:62782200-62801800	Strong transcription	GM12878-XiMat	blood
38	chr12:62782400-62793200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:62782600-62793800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:62782600-62795200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:62782600-62802400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr12:62782800-62794200	Strong transcription	Adipose Nuclei	Adipose
43	chr12:62782800-62798400	Strong transcription	HSMM	muscle
44	chr12:62782800-62799200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr12:62782800-62801200	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:62782800-62802000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:62783000-62791200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:62783200-62798800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:62783400-62791400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:62783400-62803400	Weak transcription	NHEK	skin

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