Variant report

Variant	rs225255
Chromosome Location	chr17:33955243-33955244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:33921434..33923649-chr17:33954336..33955867,2	K562	blood:
2	chr17:33954511..33957116-chr17:33962502..33964057,2	K562	blood:
3	chr17:33949132..33951570-chr17:33954798..33957288,2	K562	blood:
4	chr17:33946407..33948892-chr17:33953816..33956714,3	K562	blood:
5	chr17:33952642..33955408-chr17:33957507..33960024,3	K562	blood:

Variant related genes	Relation type
ENSG00000006125	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1049379	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12150359	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1476553	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs161182	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161183	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs161184	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1634684	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs167691	0.81[ASN][1000 genomes]
rs178649	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2124246	0.81[ASN][1000 genomes]
rs2124247	0.80[ASN][1000 genomes]
rs225245	0.89[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs225269	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225272	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225273	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225281	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225282	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225293	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225299	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225302	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs226088	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs226426	0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs226428	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs226432	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs226434	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs226439	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs226441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2285742	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2301730	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs321596	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs321599	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs321601	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs321607	0.81[CEU][hapmap]
rs321616	0.85[CEU][hapmap]
rs321617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs321618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3890901	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4795085	0.81[EUR][1000 genomes]
rs4796103	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505489	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505490	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6505491	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505492	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6505493	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71366475	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs720774	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7217565	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7221081	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7221096	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7406966	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8064556	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8067294	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8073375	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8078905	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9635770	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv1062793	chr17:33944732-33976685	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs225255	TBC1D29	cis	cerebellum	SCAN
rs225255	AP2B1	cis	Muscle Skeletal	GTEx
rs225255	PEX12	cis	cerebellum	SCAN
rs225255	TBC1D29	cis	parietal	SCAN
rs225255	SLFN5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33916800-34001200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:33920600-33969800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr17:33920800-33975800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr17:33921000-34024400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:33931000-34040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:33933000-33967400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr17:33933000-33997800	Weak transcription	Esophagus	oesophagus
8	chr17:33933600-33967400	Weak transcription	Gastric	stomach
9	chr17:33936800-33956800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr17:33937400-33965000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr17:33940000-33960000	Weak transcription	Right Ventricle	heart
12	chr17:33943400-33956800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr17:33943600-33956800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr17:33944600-33957400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr17:33947000-33958200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr17:33948400-33973400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr17:33948600-33958200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr17:33948600-33973600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr17:33948800-34010600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr17:33949000-33986400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr17:33949200-34001200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr17:33949800-33958800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr17:33950000-33957200	Strong transcription	Osteobl	bone
24	chr17:33950200-33957200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr17:33950200-33957800	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr17:33950400-33957400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr17:33950400-33965400	Strong transcription	HSMM	muscle
28	chr17:33950600-33957200	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr17:33950600-33957200	Strong transcription	HMEC	breast
30	chr17:33950600-33957200	Strong transcription	NHDF-Ad	bronchial
31	chr17:33950600-33958200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr17:33950600-33959000	Strong transcription	Placenta	Placenta
33	chr17:33950600-33959000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr17:33950600-33968600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr17:33950600-33973400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr17:33950800-33955400	Strong transcription	NH-A	brain
37	chr17:33950800-33955800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr17:33950800-33956800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr17:33950800-33957200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr17:33950800-33958000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr17:33950800-33958200	Strong transcription	Fetal Lung	lung
42	chr17:33950800-33958200	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr17:33950800-33959000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr17:33950800-33959200	Strong transcription	K562	blood
45	chr17:33950800-33959400	Strong transcription	Dnd41	blood
46	chr17:33950800-33973400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr17:33950800-33975400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr17:33950800-33975800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr17:33950800-33978800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr17:33951000-33958200	Strong transcription	Primary T cells from cord blood	blood

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