Variant report

Variant	rs2216470
Chromosome Location	chr12:46101115-46101116
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:46099342..46103099-chr12:46119888..46123799,6	MCF-7	breast:
2	chr12:46099820..46102733-chr12:46118452..46120199,2	K562	blood:

Variant related genes	Relation type
ENSG00000273015	Chromatin interaction
ENSG00000189079	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10880855	0.82[JPT][hapmap]
rs11183170	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11183175	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11183184	0.85[CEU][hapmap];0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs11183201	0.82[JPT][hapmap]
rs12314770	0.80[YRI][hapmap]
rs12582799	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1468993	0.81[JPT][hapmap]
rs1558982	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1558983	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1863127	0.83[CHD][hapmap]
rs2193749	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs2216471	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768657	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7138997	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs7958600	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7979398	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs978689	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899052	chr12:46068394-46175469	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
2	nsv899053	chr12:46100053-46141372	Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2216470	SLC38A1	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46095800-46106800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:46097200-46114600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:46097800-46118800	Weak transcription	Fetal Muscle Leg	muscle
4	chr12:46098200-46106000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr12:46098800-46101400	Enhancers	Fetal Heart	heart
6	chr12:46099000-46103400	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr12:46099600-46105600	Weak transcription	Left Ventricle	heart
8	chr12:46099600-46113000	Weak transcription	Psoas Muscle	Psoas
9	chr12:46099600-46115600	Weak transcription	Ovary	ovary
10	chr12:46100000-46102400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:46100400-46101400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:46100400-46101400	Enhancers	Brain Substantia Nigra	brain
13	chr12:46100600-46101400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
14	chr12:46100600-46104000	Enhancers	Liver	Liver
15	chr12:46100600-46118800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:46100800-46101600	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr12:46101000-46101200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:46101000-46101200	Enhancers	Brain Cingulate Gyrus	brain
19	chr12:46101000-46101400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr12:46101000-46102600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr12:46101000-46102600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr12:46101000-46112400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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