Variant report

Variant	rs6781371
Chromosome Location	chr3:160523671-160523672
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	chr3:160521593..160523754-chr3:160526329..160528531,2	MCF-7	breast:
2	chr3:160518067..160520836-chr3:160522097..160523990,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12486979	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12637922	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[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13073659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1378654	0.81[EUR][1000 genomes]
rs1378655	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1378656	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1378657	0.81[EUR][1000 genomes]
rs1378660	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1403048	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1455869	0.80[EUR][1000 genomes]
rs1598495	0.81[EUR][1000 genomes]
rs1829716	0.80[EUR][1000 genomes]
rs1851378	0.81[EUR][1000 genomes]
rs2049214	0.82[EUR][1000 genomes]
rs2049215	0.82[EUR][1000 genomes]
rs2367242	0.89[ASW][hapmap]
rs2886905	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2886909	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6441331	0.83[AMR][1000 genomes]
rs6791128	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs6794047	0.83[EUR][1000 genomes]
rs6805905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7618832	0.81[EUR][1000 genomes]
rs7633816	0.95[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs7634342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7640231	0.82[EUR][1000 genomes]
rs7640348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7643513	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs897494	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs959960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs972909	0.82[EUR][1000 genomes]
rs9809208	0.89[ASW][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap]
rs9810290	0.89[ASW][hapmap];0.87[GIH][hapmap];0.83[LWK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs9814394	0.81[EUR][1000 genomes]
rs9815499	0.81[EUR][1000 genomes]
rs9820796	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs9833075	0.81[EUR][1000 genomes]
rs9835634	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs9883862	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[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6781371	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160515400-160526400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:160520200-160525800	Weak transcription	Liver	Liver
3	chr3:160520200-160526000	Weak transcription	Aorta	Aorta
4	chr3:160520200-160526000	Weak transcription	Brain Angular Gyrus	brain
5	chr3:160520200-160526400	Weak transcription	Stomach Mucosa	stomach
6	chr3:160520400-160526400	Weak transcription	Brain Anterior Caudate	brain
7	chr3:160520400-160529600	Weak transcription	Colonic Mucosa	Colon
8	chr3:160521000-160523800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:160521000-160523800	Weak transcription	Psoas Muscle	Psoas
10	chr3:160521000-160524000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:160521000-160526000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:160521000-160526000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:160521000-160526000	Weak transcription	Right Atrium	heart
14	chr3:160521000-160526000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:160521000-160526400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:160522000-160525200	Enhancers	Colon Smooth Muscle	Colon
17	chr3:160522200-160524400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:160522400-160523800	Enhancers	Rectal Smooth Muscle	rectum
19	chr3:160522400-160524200	Enhancers	Stomach Smooth Muscle	stomach
20	chr3:160522400-160524400	Enhancers	Adipose Nuclei	Adipose
21	chr3:160522400-160524600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:160522400-160524600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr3:160522600-160523800	Enhancers	Fetal Muscle Leg	muscle
24	chr3:160522600-160524200	Enhancers	Left Ventricle	heart
25	chr3:160522600-160524200	Enhancers	Right Ventricle	heart
26	chr3:160522800-160524000	Enhancers	Fetal Brain Male	brain
27	chr3:160522800-160525200	Weak transcription	Brain Germinal Matrix	brain
28	chr3:160522800-160525800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:160522800-160526000	Weak transcription	Gastric	stomach
30	chr3:160522800-160527600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:160522800-160529000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:160523000-160523800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:160523000-160524000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:160523000-160524000	Weak transcription	Fetal Brain Female	brain
35	chr3:160523000-160524000	Weak transcription	NHDF-Ad	bronchial
36	chr3:160523000-160525800	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:160523000-160526000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:160523000-160526000	Weak transcription	Brain Substantia Nigra	brain
39	chr3:160523000-160526000	Weak transcription	Pancreas	Pancrea
40	chr3:160523000-160526200	Weak transcription	Esophagus	oesophagus
41	chr3:160523000-160526200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:160523000-160526400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:160523000-160532800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:160523200-160526000	Weak transcription	Fetal Heart	heart
45	chr3:160523200-160526400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:160523200-160528600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:160523400-160526200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:160523400-160527400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:160523600-160523800	Enhancers	Placenta	Placenta
50	chr3:160523600-160524200	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links