Variant report

Variant	rs3801288
Chromosome Location	chr7:98945908-98945909
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	chr7:98936753..98939363-chr7:98944952..98946486,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10155966	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10225529	0.87[EUR][1000 genomes]
rs10232076	0.99[ASN][1000 genomes]
rs10236149	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10238965	0.92[CEU][hapmap];0.81[MEX][hapmap]
rs10243678	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10249167	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10255399	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10258757	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10267346	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10270459	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10270917	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10271049	0.92[CEU][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap]
rs10272998	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10274407	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10279308	0.91[CEU][hapmap]
rs1043466	0.92[CEU][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap]
rs10953286	0.94[GIH][hapmap];0.94[JPT][hapmap]
rs10953287	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11762273	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11771702	0.83[CEU][hapmap]
rs11973460	0.82[AMR][1000 genomes]
rs11976018	0.92[CEU][hapmap];0.89[MKK][hapmap]
rs11978089	0.91[CEU][hapmap]
rs12112936	0.83[CEU][hapmap]
rs12113440	0.83[CEU][hapmap]
rs13240600	0.82[CEU][hapmap]
rs17161652	0.84[JPT][hapmap]
rs17161677	0.84[JPT][hapmap]
rs17161692	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17161695	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs1980307	0.92[CEU][hapmap];0.90[MEX][hapmap]
rs2003499	0.91[CEU][hapmap]
rs2072181	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2074652	0.84[JPT][hapmap]
rs2107922	0.86[EUR][1000 genomes]
rs2240384	0.92[CEU][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap]
rs2272168	0.92[CEU][hapmap]
rs2280600	0.92[CEU][hapmap];0.90[MEX][hapmap]
rs2280601	0.92[CEU][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap]
rs2286162	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301889	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2404323	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28468623	0.98[ASN][1000 genomes]
rs28495024	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28820905	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3137	0.92[CEU][hapmap]
rs3843540	0.83[CEU][hapmap]
rs4729532	0.91[CEU][hapmap]
rs58660994	0.98[ASN][1000 genomes]
rs59725656	0.98[ASN][1000 genomes]
rs6943920	0.91[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6948775	0.99[ASN][1000 genomes]
rs6953476	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6955490	0.91[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs6962772	0.92[CEU][hapmap];0.90[MEX][hapmap]
rs6972337	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6975099	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73395547	0.98[ASN][1000 genomes]
rs73395557	0.98[ASN][1000 genomes]
rs73395580	0.99[ASN][1000 genomes]
rs733991	0.83[CEU][hapmap]
rs7794705	0.92[CEU][hapmap]
rs883403	0.92[CEU][hapmap]
rs917154	0.91[CEU][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap]
rs9641253	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9768020	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9918551	0.98[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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3801288	PILRA	cis	cerebellum	SCAN
rs3801288	ZKSCAN1	cis	parietal	SCAN
rs3801288	ARPC1B	cis	Thyroid	GTEx
rs3801288	CPSF4	cis	parietal	SCAN
rs3801288	GATS	cis	parietal	SCAN
rs3801288	ACTL6B	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98924400-98957200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:98924600-98971600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:98925200-98965200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:98927200-98966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:98927800-98960600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:98928400-98967200	Strong transcription	Fetal Thymus	thymus
7	chr7:98928600-98965200	Strong transcription	Dnd41	blood
8	chr7:98929000-98965600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr7:98929400-98965200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:98929600-98962800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr7:98929600-98965400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr7:98929800-98965000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr7:98930000-98950200	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr7:98930000-98962800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:98930000-98968200	Strong transcription	Fetal Intestine Small	intestine
16	chr7:98930200-98954600	Weak transcription	Fetal Heart	heart
17	chr7:98930200-98968400	Strong transcription	Fetal Stomach	stomach
18	chr7:98930600-98946000	Strong transcription	Osteobl	bone
19	chr7:98930600-98950400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:98930600-98965200	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr7:98930600-98965200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr7:98930600-98965200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr7:98930800-98950000	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr7:98930800-98955200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:98930800-98960200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr7:98930800-98965200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr7:98930800-98965200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr7:98930800-98965400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr7:98930800-98966800	Strong transcription	Adipose Nuclei	Adipose
30	chr7:98930800-98967000	Strong transcription	Fetal Muscle Leg	muscle
31	chr7:98930800-98967600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr7:98931000-98950400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr7:98931000-98953400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr7:98931000-98959600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:98931000-98960200	Strong transcription	Placenta	Placenta
36	chr7:98931000-98965000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:98931200-98951200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr7:98931400-98947400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr7:98932600-98966400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:98933000-98950000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:98934200-98950400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr7:98934400-98965200	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr7:98935600-98971600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr7:98937600-98946000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:98937600-98955200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr7:98937800-98946000	Weak transcription	Small Intestine	intestine
47	chr7:98938200-98949400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr7:98938200-98955200	Weak transcription	Stomach Mucosa	stomach
49	chr7:98938400-98947000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr7:98938600-98946400	Weak transcription	Fetal Brain Male	brain

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