Variant report

Variant	rs6440741
Chromosome Location	chr3:151134540-151134541
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:151133170..151135027-chr3:151147845..151150595,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10935848	0.97[ASN][1000 genomes]
rs13088575	0.82[CEU][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs16863260	1.00[YRI][hapmap]
rs2087728	0.88[ASN][1000 genomes]
rs2101647	0.88[ASN][1000 genomes]
rs2172250	0.89[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs3975409	0.88[ASN][1000 genomes]
rs4680440	0.82[CEU][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs4680442	0.82[CEU][hapmap];0.89[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs4680443	0.82[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs6440743	0.97[ASN][1000 genomes]
rs6792496	0.94[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7611956	0.89[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs7621591	0.82[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap]
rs7652056	0.86[ASN][1000 genomes]
rs9289838	0.82[CEU][hapmap]
rs937119	0.93[ASN][1000 genomes]
rs937120	0.84[ASN][1000 genomes]
rs937127	0.89[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs9840738	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs9873499	0.82[EUR][1000 genomes]
rs9877298	0.82[CEU][hapmap]
rs9878370	0.86[ASN][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	nsv829757	chr3:151044880-151226442	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1000355	chr3:151108859-151243835	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv995048	chr3:151114074-151560019	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6440741	MED12L	cis	intralobular white matter	BrainEAC

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151075600-151136400	Weak transcription	Fetal Brain Female	brain
2	chr3:151090200-151142400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr3:151098800-151143400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:151102200-151148600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:151102800-151136400	Weak transcription	Brain Substantia Nigra	brain
6	chr3:151102800-151150600	Weak transcription	Brain Anterior Caudate	brain
7	chr3:151104200-151139600	Weak transcription	Dnd41	blood
8	chr3:151106000-151154600	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:151112800-151143400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:151113200-151142600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:151113400-151143600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:151117600-151142600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:151119000-151142600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:151121800-151138400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:151122600-151135400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:151122800-151139800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:151123200-151139600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:151124600-151139200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:151126800-151140200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:151126800-151148600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:151127200-151149200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:151129400-151137800	Weak transcription	Placenta	Placenta
23	chr3:151129400-151142400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:151129400-151162800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:151130800-151142600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:151131600-151135600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:151132000-151148800	Weak transcription	Fetal Intestine Small	intestine
28	chr3:151132400-151134800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:151132400-151135600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:151132400-151137600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:151132400-151142400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:151133200-151142600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:151133400-151148600	Weak transcription	Brain Germinal Matrix	brain
34	chr3:151133400-151154800	Weak transcription	Fetal Brain Male	brain
35	chr3:151133600-151142600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:151133600-151151800	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:151134400-151135000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links