Variant report

Variant	rs620321
Chromosome Location	chr9:79315400-79315401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79306577..79308697-chr9:79313991..79316581,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106772	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10869799	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500952	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs505034	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[ASN][1000 genomes]
rs506086	0.89[CEU][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs509489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs512110	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517634	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556725	0.88[CEU][hapmap];0.85[ASN][1000 genomes]
rs560094	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561970	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566584	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572737	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591411	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594498	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594586	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs611461	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs615187	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs618145	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620476	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620552	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620737	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625981	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs626416	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs646698	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650682	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs677913	0.89[ASN][1000 genomes]
rs678943	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs680729	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680775	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018971	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7033978	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870516	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893481	chr9:79304043-79348193	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs620321	PSAT1	cis	parietal	SCAN
rs620321	PRUNE2	cis	Whole Blood	GTEx
rs620321	C9orf85	cis	parietal	SCAN
rs620321	C9orf85	cis	cerebellum	SCAN
rs620321	GCNT1	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:79307400-79315800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:79307400-79317600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:79307600-79315800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:79307800-79316000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr9:79308000-79315800	Weak transcription	Aorta	Aorta
7	chr9:79308000-79315800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:79309200-79315600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:79312000-79316600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr9:79313000-79316000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr9:79314200-79316000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:79314200-79316800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:79314200-79320000	Enhancers	Fetal Brain Male	brain
14	chr9:79314400-79316000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr9:79314400-79316000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr9:79314400-79316200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr9:79314400-79316600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:79314400-79316800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:79314400-79316800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:79314400-79316800	Enhancers	Brain Anterior Caudate	brain
21	chr9:79314400-79316800	Enhancers	Osteobl	bone
22	chr9:79314400-79317200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:79314400-79317800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr9:79314400-79317800	Genic enhancers	HSMMtube	muscle
25	chr9:79314400-79318800	Enhancers	Fetal Muscle Leg	muscle
26	chr9:79314600-79315400	Enhancers	Colon Smooth Muscle	Colon
27	chr9:79314600-79315400	Enhancers	Fetal Lung	lung
28	chr9:79314600-79316800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr9:79314600-79316800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr9:79314600-79317600	Enhancers	NHDF-Ad	bronchial
31	chr9:79314800-79316600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:79314800-79316600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:79314800-79316800	Enhancers	Brain Angular Gyrus	brain
34	chr9:79314800-79316800	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr9:79314800-79316800	Enhancers	NH-A	brain
36	chr9:79314800-79317000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:79314800-79317200	Enhancers	Brain Hippocampus Middle	brain
38	chr9:79314800-79317600	Genic enhancers	HSMM	muscle
39	chr9:79314800-79318800	Enhancers	Fetal Stomach	stomach
40	chr9:79315000-79316200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:79315000-79316200	Weak transcription	Fetal Brain Female	brain
42	chr9:79315000-79317000	Enhancers	HUVEC	blood vessel
43	chr9:79315000-79318000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr9:79315200-79315400	Enhancers	Fetal Kidney	kidney
45	chr9:79315200-79315600	Weak transcription	Fetal Thymus	thymus
46	chr9:79315200-79316000	Weak transcription	Brain Substantia Nigra	brain
47	chr9:79315200-79316200	Weak transcription	Psoas Muscle	Psoas
48	chr9:79315200-79319400	Weak transcription	Stomach Mucosa	stomach
49	chr9:79315200-79319600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr9:79315200-79327600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links