Variant report

Variant	rs12139610
Chromosome Location	chr1:171696112-171696113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10798598	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10798599	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10798603	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913488	0.81[EUR][1000 genomes]
rs10913508	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913530	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913559	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913586	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11583530	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11805692	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806314	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045452	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12096984	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12120152	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2073484	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227229	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4342884	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4468194	0.94[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]
rs6665581	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6668623	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672082	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6673782	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674468	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674688	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674774	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6682452	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6685742	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6688447	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs763225	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs999685	0.94[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
rs12139610	VAMP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171665600-171705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:171665600-171708800	Weak transcription	Brain Angular Gyrus	brain
3	chr1:171666000-171705400	Weak transcription	Pancreas	Pancrea
4	chr1:171666800-171702400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:171668800-171705400	Weak transcription	Right Ventricle	heart
6	chr1:171668800-171708200	Weak transcription	Small Intestine	intestine
7	chr1:171669600-171705400	Weak transcription	Fetal Brain Male	brain
8	chr1:171674000-171696400	Weak transcription	HSMM	muscle
9	chr1:171674800-171696800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:171674800-171697200	Weak transcription	Ovary	ovary
11	chr1:171677200-171698800	Weak transcription	Aorta	Aorta
12	chr1:171686000-171696800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:171686000-171699000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:171686400-171696800	Weak transcription	NH-A	brain
15	chr1:171686600-171710400	Weak transcription	Esophagus	oesophagus
16	chr1:171686600-171710400	Weak transcription	Gastric	stomach
17	chr1:171686800-171704600	Weak transcription	NHEK	skin
18	chr1:171687000-171696200	Weak transcription	Placenta	Placenta
19	chr1:171687000-171704600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:171687600-171696600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:171687600-171704600	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:171687600-171708000	Weak transcription	K562	blood
23	chr1:171687800-171696400	Weak transcription	NHLF	lung
24	chr1:171688400-171698800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:171690800-171699000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:171691800-171696400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:171692400-171696400	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:171692400-171696600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:171692400-171697000	Weak transcription	Left Ventricle	heart
30	chr1:171692400-171705800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:171692400-171708400	Weak transcription	Brain Substantia Nigra	brain
32	chr1:171692400-171710400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:171692400-171710400	Weak transcription	Lung	lung
34	chr1:171692600-171696200	Weak transcription	Dnd41	blood
35	chr1:171692600-171696400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:171692600-171696400	Weak transcription	Fetal Brain Female	brain
37	chr1:171692600-171696400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:171692600-171696600	Weak transcription	Brain Anterior Caudate	brain
39	chr1:171692600-171699000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr1:171692600-171705000	Weak transcription	Thymus	Thymus
41	chr1:171692600-171705400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:171692600-171705600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:171692600-171708400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:171692600-171709800	Weak transcription	Stomach Mucosa	stomach
45	chr1:171692600-171710200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr1:171692800-171696200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:171692800-171696400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:171692800-171696400	Weak transcription	Adipose Nuclei	Adipose
49	chr1:171692800-171696400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:171692800-171696400	Weak transcription	Fetal Lung	lung

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