Variant report

Variant	rs1001373
Chromosome Location	chr1:171684506-171684507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171683036..171685816-chr1:171686230..171688004,2	MCF-7	breast:
2	chr1:171611915..171613655-chr1:171683755..171685490,3	MCF-7	breast:
3	chr1:171613978..171614654-chr1:171684466..171685390,3	MCF-7	breast:
4	chr1:171682877..171685651-chr1:171749605..171752042,3	K562	blood:

Variant related genes	Relation type
ENSG00000010165	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10157798	0.82[CHD][hapmap]
rs10489249	1.00[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10489251	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1052676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10903	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913489	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10913490	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10913492	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10913511	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913514	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913529	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913578	0.89[GIH][hapmap];0.83[JPT][hapmap]
rs10913582	1.00[CEU][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10913587	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11576221	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11577073	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11577197	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11577745	1.00[CEU][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11578179	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11578699	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11578723	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11579698	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11580415	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11580522	1.00[CEU][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11583920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590680	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11590714	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11799420	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11799938	0.86[CHD][hapmap]
rs11799961	0.84[CHD][hapmap]
rs11801846	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11803174	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11808099	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811780	0.85[EUR][1000 genomes]
rs12119232	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12123727	0.83[EUR][1000 genomes]
rs12127026	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12128536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12132221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15655	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16843251	0.81[GIH][hapmap];0.83[JPT][hapmap]
rs17649050	1.00[CEU][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17649068	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17649250	1.00[CEU][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs2298914	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2421911	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3753539	0.88[GIH][hapmap];0.83[JPT][hapmap]
rs3766653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55670848	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58455759	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6656003	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659874	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6662720	1.00[CEU][hapmap]
rs6667559	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6669263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6670427	1.00[CEU][hapmap]
rs6678890	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6679354	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7528057	0.83[EUR][1000 genomes]
rs7536436	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7536543	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9661596	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9662174	0.81[EUR][1000 genomes]
rs9662506	1.00[CEU][hapmap]
rs9662853	0.83[AMR][1000 genomes];0.84[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1001373	METTL13	cis	parietal	SCAN
rs1001373	VAMP4	cis	Frontal Cortex	GTEx
rs1001373	PRDX6	cis	parietal	SCAN
rs1001373	VAMP4	Cis_1M	lymphoblastoid	RTeQTL
rs1001373	VAMP4	cis	Brain Pons	GTEx
rs1001373	BCHE	trans	lymphoblastoid	seeQTL
rs1001373	VAMP4	cis	lymphoblastoid	seeQTL
rs1001373	VAMP4	cis	Temporal Cortex	GTEx
rs1001373	VAMP4	cis	multi-tissue	Pritchard

Chromatin state (count:100 , 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	chr1:171664800-171684800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:171665000-171692000	Weak transcription	Brain Substantia Nigra	brain
4	chr1:171665600-171705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:171665600-171708800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:171666000-171685000	Weak transcription	Brain Germinal Matrix	brain
7	chr1:171666000-171705400	Weak transcription	Pancreas	Pancrea
8	chr1:171666200-171684600	Weak transcription	Fetal Stomach	stomach
9	chr1:171666200-171684800	Weak transcription	Thymus	Thymus
10	chr1:171666600-171684800	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:171666600-171686200	Weak transcription	Gastric	stomach
12	chr1:171666800-171686800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:171666800-171692000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:171666800-171692000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:171666800-171692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:171666800-171702400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:171667000-171685000	Weak transcription	Osteobl	bone
18	chr1:171667000-171692000	Weak transcription	Fetal Brain Female	brain
19	chr1:171667000-171692200	Weak transcription	Brain Anterior Caudate	brain
20	chr1:171667600-171692000	Weak transcription	Fetal Lung	lung
21	chr1:171667800-171688400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:171667800-171688800	Weak transcription	Spleen	Spleen
23	chr1:171667800-171692000	Weak transcription	Fetal Thymus	thymus
24	chr1:171668000-171685800	Weak transcription	Esophagus	oesophagus
25	chr1:171668600-171684800	Weak transcription	Fetal Kidney	kidney
26	chr1:171668600-171692400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:171668800-171705400	Weak transcription	Right Ventricle	heart
28	chr1:171668800-171708200	Weak transcription	Small Intestine	intestine
29	chr1:171669400-171685800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:171669600-171685800	Weak transcription	NHEK	skin
31	chr1:171669600-171705400	Weak transcription	Fetal Brain Male	brain
32	chr1:171670000-171688200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:171670600-171685600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:171670600-171692000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:171671200-171685000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:171672800-171685800	Weak transcription	K562	blood
37	chr1:171672800-171686200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:171672800-171692000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:171673600-171686800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:171674000-171696400	Weak transcription	HSMM	muscle
41	chr1:171674200-171686000	Weak transcription	Stomach Mucosa	stomach
42	chr1:171674600-171684800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:171674600-171686000	Weak transcription	HSMMtube	muscle
44	chr1:171674600-171692200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr1:171674800-171696800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:171674800-171697200	Weak transcription	Ovary	ovary
47	chr1:171675200-171685000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:171675200-171686200	Weak transcription	Psoas Muscle	Psoas
49	chr1:171675400-171685800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:171676800-171685800	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links