Variant report

Variant	rs10272998
Chromosome Location	chr7:98933918-98933919
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:98933693..98936414-chr7:98989048..98991097,2	MCF-7	breast:
2	chr7:98921929..98925075-chr7:98932538..98936577,3	MCF-7	breast:
3	chr7:98933721..98935739-chr7:98944063..98945648,2	K562	blood:

Variant related genes	Relation type
ENSG00000241685	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10155966	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10225529	0.87[EUR][1000 genomes]
rs10232076	0.98[ASN][1000 genomes]
rs10236149	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10243678	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10249167	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10255399	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10258757	0.91[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10267346	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10270459	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10270917	0.91[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10271049	0.82[ASW][hapmap];0.92[CEU][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap]
rs10274407	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10279308	0.91[CEU][hapmap]
rs1043466	0.82[ASW][hapmap];0.92[CEU][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap]
rs10953286	0.82[ASW][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap]
rs10953287	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11762273	0.91[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11771702	0.83[CEU][hapmap]
rs11976018	0.82[ASW][hapmap];0.92[CEU][hapmap];0.92[MKK][hapmap]
rs11978089	0.91[CEU][hapmap]
rs12112936	0.83[CEU][hapmap]
rs12113440	0.83[CEU][hapmap]
rs13240600	0.82[CEU][hapmap]
rs17161652	0.85[JPT][hapmap]
rs17161677	0.85[JPT][hapmap]
rs17161692	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17161695	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs1980307	0.82[ASW][hapmap];0.92[CEU][hapmap];0.90[MEX][hapmap]
rs2003499	0.91[CEU][hapmap]
rs2072181	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2074652	0.85[JPT][hapmap]
rs2107922	0.86[EUR][1000 genomes]
rs2240384	0.82[ASW][hapmap];0.92[CEU][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap]
rs2272168	0.92[CEU][hapmap]
rs2280600	0.92[CEU][hapmap];0.90[MEX][hapmap]
rs2280601	0.82[ASW][hapmap];0.92[CEU][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap]
rs2286162	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2301889	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2404323	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28468623	0.99[ASN][1000 genomes]
rs28495024	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28820905	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3137	0.92[CEU][hapmap]
rs3801288	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]
rs3843540	0.83[CEU][hapmap]
rs4729532	0.83[ASW][hapmap];0.91[CEU][hapmap]
rs58660994	0.99[ASN][1000 genomes]
rs59725656	0.97[ASN][1000 genomes]
rs6943920	0.91[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6948775	0.98[ASN][1000 genomes]
rs6953476	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955490	0.83[ASW][hapmap];0.91[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs6962772	0.82[ASW][hapmap];0.92[CEU][hapmap];0.90[MEX][hapmap]
rs6972337	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975099	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73395547	0.99[ASN][1000 genomes]
rs73395557	0.99[ASN][1000 genomes]
rs73395580	0.98[ASN][1000 genomes]
rs733991	0.83[CEU][hapmap]
rs7794705	0.92[CEU][hapmap]
rs883403	0.92[CEU][hapmap]
rs917154	0.82[ASW][hapmap];0.91[CEU][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap]
rs9641253	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9768020	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9918551	0.97[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
rs10272998	ARPC1B	cis	Thyroid	GTEx
rs10272998	CPSF4	cis	parietal	SCAN
rs10272998	GATS	cis	parietal	SCAN
rs10272998	ZKSCAN1	cis	parietal	SCAN
rs10272998	PILRA	cis	cerebellum	SCAN
rs10272998	ACTL6B	cis	cerebellum	SCAN

Chromatin state (count:124 , 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	chr7:98924800-98935600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr7:98924800-98935600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr7:98924800-98935800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:98924800-98936200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:98925200-98965200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:98925400-98935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:98925600-98936200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:98926200-98934200	Weak transcription	Spleen	Spleen
11	chr7:98926400-98935600	Weak transcription	Brain Substantia Nigra	brain
12	chr7:98926400-98935800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:98926600-98941600	Weak transcription	Psoas Muscle	Psoas
14	chr7:98927200-98966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:98927400-98935400	Weak transcription	HSMMtube	muscle
16	chr7:98927400-98936400	Weak transcription	Colon Smooth Muscle	Colon
17	chr7:98927600-98934200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr7:98927600-98944200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:98927800-98960600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:98928200-98938600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr7:98928400-98934800	Weak transcription	HepG2	liver
22	chr7:98928400-98967200	Strong transcription	Fetal Thymus	thymus
23	chr7:98928600-98965200	Strong transcription	Dnd41	blood
24	chr7:98929000-98935800	Weak transcription	Pancreas	Pancrea
25	chr7:98929000-98965600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:98929400-98938600	Strong transcription	K562	blood
27	chr7:98929400-98965200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr7:98929600-98938600	Strong transcription	GM12878-XiMat	blood
29	chr7:98929600-98962800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr7:98929600-98965400	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr7:98929800-98935200	Weak transcription	HMEC	breast
32	chr7:98929800-98935800	Weak transcription	NHLF	lung
33	chr7:98929800-98965000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr7:98930000-98936400	Weak transcription	Stomach Mucosa	stomach
35	chr7:98930000-98950200	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr7:98930000-98962800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr7:98930000-98968200	Strong transcription	Fetal Intestine Small	intestine
38	chr7:98930200-98935400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:98930200-98936800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:98930200-98954600	Weak transcription	Fetal Heart	heart
41	chr7:98930200-98968400	Strong transcription	Fetal Stomach	stomach
42	chr7:98930400-98938600	Strong transcription	Fetal Intestine Large	intestine
43	chr7:98930600-98938600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr7:98930600-98938600	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:98930600-98946000	Strong transcription	Osteobl	bone
46	chr7:98930600-98950400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr7:98930600-98965200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr7:98930600-98965200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr7:98930600-98965200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr7:98930800-98934600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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