Variant report

Variant	rs10913514
Chromosome Location	chr1:171670823-171670824
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171667939..171671943-chr1:171675100..171678672,3	K562	blood:
2	chr1:171665381..171668263-chr1:171669803..171671698,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1001373	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10489249	0.91[EUR][1000 genomes]
rs10489251	0.92[EUR][1000 genomes]
rs1052676	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10903	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913489	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10913490	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10913492	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10913507	0.80[EUR][1000 genomes]
rs10913511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913529	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913565	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10913582	0.92[EUR][1000 genomes]
rs10913587	0.92[EUR][1000 genomes]
rs11576221	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11577073	0.92[EUR][1000 genomes]
rs11577197	0.92[EUR][1000 genomes]
rs11577745	0.92[EUR][1000 genomes]
rs11578179	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11578699	0.92[EUR][1000 genomes]
rs11578723	0.92[EUR][1000 genomes]
rs11579698	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11580415	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11580522	0.92[EUR][1000 genomes]
rs11583920	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11590680	0.92[EUR][1000 genomes]
rs11590714	0.92[EUR][1000 genomes]
rs11799420	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11801846	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803174	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808099	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11811780	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12119232	0.93[EUR][1000 genomes]
rs12123727	0.84[EUR][1000 genomes]
rs12127026	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128536	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132221	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs15655	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649050	0.92[EUR][1000 genomes]
rs17649068	0.91[EUR][1000 genomes]
rs2298914	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2421911	0.88[EUR][1000 genomes]
rs3766653	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55670848	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58455759	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656003	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6659874	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6667559	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6669263	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6678890	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6679354	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528057	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7536436	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7536543	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9661596	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9662174	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9662853	0.87[AMR][1000 genomes];0.88[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10913514	VAMP4	Cis_1M	lymphoblastoid	RTeQTL
rs10913514	VAMP4	cis	multi-tissue	Pritchard

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171664400-171685800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:171664600-171674400	Weak transcription	Primary T cells from cord blood	blood
3	chr1:171664800-171684800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:171665000-171692000	Weak transcription	Brain Substantia Nigra	brain
5	chr1:171665400-171674600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:171665600-171705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:171665600-171708800	Weak transcription	Brain Angular Gyrus	brain
8	chr1:171666000-171674200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:171666000-171676000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:171666000-171676600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:171666000-171685000	Weak transcription	Brain Germinal Matrix	brain
12	chr1:171666000-171705400	Weak transcription	Pancreas	Pancrea
13	chr1:171666200-171676000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:171666200-171682600	Weak transcription	Lung	lung
15	chr1:171666200-171684600	Weak transcription	Fetal Stomach	stomach
16	chr1:171666200-171684800	Weak transcription	Thymus	Thymus
17	chr1:171666400-171673000	Weak transcription	Primary B cells from cord blood	blood
18	chr1:171666600-171676600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:171666600-171684800	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:171666600-171686200	Weak transcription	Gastric	stomach
21	chr1:171666800-171671800	Weak transcription	Liver	Liver
22	chr1:171666800-171673600	Weak transcription	HSMM	muscle
23	chr1:171666800-171674200	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:171666800-171674200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:171666800-171675600	Weak transcription	Colonic Mucosa	Colon
26	chr1:171666800-171679200	Weak transcription	NH-A	brain
27	chr1:171666800-171686800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:171666800-171692000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:171666800-171692000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:171666800-171692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:171666800-171702400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:171667000-171672600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:171667000-171672800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:171667000-171675800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr1:171667000-171676600	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:171667000-171676800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:171667000-171685000	Weak transcription	Osteobl	bone
38	chr1:171667000-171692000	Weak transcription	Fetal Brain Female	brain
39	chr1:171667000-171692200	Weak transcription	Brain Anterior Caudate	brain
40	chr1:171667200-171672800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr1:171667600-171674400	Weak transcription	Placenta	Placenta
42	chr1:171667600-171676200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr1:171667600-171681200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:171667600-171692000	Weak transcription	Fetal Lung	lung
45	chr1:171667800-171676400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:171667800-171688400	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr1:171667800-171688800	Weak transcription	Spleen	Spleen
48	chr1:171667800-171692000	Weak transcription	Fetal Thymus	thymus
49	chr1:171668000-171674400	Weak transcription	HSMMtube	muscle
50	chr1:171668000-171685800	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links