Variant report

Variant	rs12485328
Chromosome Location	chr3:156360259-156360260
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	chr3:156357866..156360454-chr3:156391073..156393426,2	MCF-7	breast:
2	chr3:156351719..156355141-chr3:156359193..156362259,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSR3-7	chr3:156359231-156383752	predAs_chen_BG181400_1

Variant related genes	Relation type
ENSG00000243926	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11709829	0.90[YRI][hapmap]
rs12488285	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12696042	0.83[CEU][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13073442	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13092225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1469536	0.89[YRI][hapmap]
rs1510276	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1510279	0.89[ASN][1000 genomes]
rs1510280	0.87[ASN][1000 genomes]
rs1850721	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2136690	0.91[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs28493995	0.89[ASN][1000 genomes]
rs6441091	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6766154	0.91[CEU][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6772236	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6778962	0.92[JPT][hapmap]
rs6790457	0.92[JPT][hapmap]
rs6807894	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7617108	0.90[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7628802	0.92[JPT][hapmap]
rs7638768	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7639306	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9815389	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9822953	0.83[CEU][hapmap]
rs9834214	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9835981	0.87[ASN][1000 genomes]
rs9838430	0.83[CEU][hapmap]
rs9852504	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs985855	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs985856	0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156348800-156360600	Weak transcription	Right Atrium	heart
2	chr3:156349400-156361000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:156351800-156361000	Weak transcription	Fetal Stomach	stomach
4	chr3:156355800-156367800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:156356200-156361200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:156356200-156361600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:156357400-156360600	Weak transcription	K562	blood
8	chr3:156358800-156361200	Enhancers	GM12878-XiMat	blood
9	chr3:156359000-156360600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:156359000-156360600	Weak transcription	Osteobl	bone
11	chr3:156359000-156361400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr3:156359000-156362000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr3:156359200-156360800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:156359600-156361000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:156360000-156360400	Weak transcription	Fetal Heart	heart
16	chr3:156360000-156361200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:156360000-156361600	Enhancers	Primary hematopoietic stem cells	blood
18	chr3:156360000-156376600	Weak transcription	Psoas Muscle	Psoas
19	chr3:156360200-156360600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:156360200-156360600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:156360200-156362200	Enhancers	Primary neutrophils fromperipheralblood	blood

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