Variant report

Variant	rs2227229
Chromosome Location	chr1:171686486-171686487
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	chr1:171683036..171685816-chr1:171686230..171688004,2	MCF-7	breast:
2	chr1:171686305..171689252-chr1:171710111..171712104,2	K562	blood:

Variant related genes	Relation type
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10798598	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10798599	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10798603	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913488	0.81[EUR][1000 genomes]
rs10913508	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913530	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913559	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913578	0.86[YRI][hapmap]
rs10913586	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11583530	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11805692	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806314	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045452	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12096984	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12120152	1.00[CEU][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12139610	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843251	0.90[YRI][hapmap]
rs2073484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753539	0.86[YRI][hapmap]
rs4342884	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4468194	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425400	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6659539	0.82[EUR][1000 genomes]
rs6662836	0.95[CEU][hapmap];0.85[JPT][hapmap]
rs6665581	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6668623	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672082	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6673782	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674468	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674688	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674774	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6682452	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6685742	0.90[CEU][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6688447	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6700606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs763225	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9659578	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs9943293	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs999685	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1800458	chr1:171667663-171701129	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2227229	VAMP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171665000-171692000	Weak transcription	Brain Substantia Nigra	brain
2	chr1:171665600-171705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:171665600-171708800	Weak transcription	Brain Angular Gyrus	brain
4	chr1:171666000-171705400	Weak transcription	Pancreas	Pancrea
5	chr1:171666800-171686800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:171666800-171692000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:171666800-171692000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:171666800-171692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:171666800-171702400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:171667000-171692000	Weak transcription	Fetal Brain Female	brain
11	chr1:171667000-171692200	Weak transcription	Brain Anterior Caudate	brain
12	chr1:171667600-171692000	Weak transcription	Fetal Lung	lung
13	chr1:171667800-171688400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr1:171667800-171688800	Weak transcription	Spleen	Spleen
15	chr1:171667800-171692000	Weak transcription	Fetal Thymus	thymus
16	chr1:171668600-171692400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:171668800-171705400	Weak transcription	Right Ventricle	heart
18	chr1:171668800-171708200	Weak transcription	Small Intestine	intestine
19	chr1:171669600-171705400	Weak transcription	Fetal Brain Male	brain
20	chr1:171670000-171688200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:171670600-171692000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:171672800-171692000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:171673600-171686800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:171674000-171696400	Weak transcription	HSMM	muscle
25	chr1:171674600-171692200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:171674800-171696800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:171674800-171697200	Weak transcription	Ovary	ovary
28	chr1:171677000-171692000	Weak transcription	GM12878-XiMat	blood
29	chr1:171677200-171692000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr1:171677200-171692200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:171677200-171698800	Weak transcription	Aorta	Aorta
32	chr1:171677400-171692200	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:171678000-171692000	Weak transcription	Fetal Intestine Small	intestine
34	chr1:171678800-171692000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:171679000-171687200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:171679000-171692000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:171679000-171693800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:171679000-171696000	Weak transcription	Fetal Intestine Large	intestine
39	chr1:171680200-171688600	Strong transcription	Primary B cells from cord blood	blood
40	chr1:171681800-171688200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr1:171682000-171687600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr1:171682200-171686800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:171682600-171687600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:171683000-171687800	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:171683200-171692800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:171683400-171687000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:171683800-171687000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:171684000-171688200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr1:171684400-171686600	Strong transcription	Adipose Nuclei	Adipose
50	chr1:171684400-171687600	Enhancers	Colon Smooth Muscle	Colon

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