Variant report

Variant	rs10489249
Chromosome Location	chr1:171714521-171714522
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:171714374-171714574	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:171714445-171715689	K562	blood:	n/a	n/a
3	STAT3	chr1:171714153-171714536	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:171714147-171714989	MCF10A-Er-Src	breast:	n/a	chr1:171714858-171714869
5	FOS	chr1:171714120-171714540	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:171713530-171715114	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:171710341..171715416-chr1:171748571..171752440,7	MCF-7	breast:
2	chr1:171709915..171712765-chr1:171713843..171716180,3	MCF-7	breast:
3	chr1:171709343..171715185-chr1:171748592..171756289,15	K562	blood:
4	chr1:171710254..171714548-chr1:171728803..171733052,4	K562	blood:
5	chr1:171709981..171712025-chr1:171713091..171714877,2	K562	blood:
6	chr1:171712949..171715185-chr1:171753608..171756289,2	K562	blood:
7	chr1:171711002..171712859-chr1:171714467..171716511,2	MCF-7	breast:
8	chr1:171710037..171714996-chr1:171734843..171738629,6	MCF-7	breast:

No data

Variant related genes	Relation type
VAMP4	TF binding region
ENSG00000253060	Chromatin interaction
ENSG00000117533	Chromatin interaction
ENSG00000236741	Chromatin interaction
ENSG00000010165	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1001373	1.00[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10489251	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052676	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10753181	0.99[ASN][1000 genomes]
rs10903	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10913511	0.91[EUR][1000 genomes]
rs10913514	0.91[EUR][1000 genomes]
rs10913529	1.00[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10913565	1.00[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10913578	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10913582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913587	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913625	0.85[YRI][hapmap]
rs11576221	1.00[CEU][hapmap]
rs11577073	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577197	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578179	0.91[EUR][1000 genomes]
rs11578699	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578723	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579698	0.92[EUR][1000 genomes]
rs11580415	0.92[EUR][1000 genomes]
rs11580522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583920	1.00[CEU][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11590680	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590714	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801846	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11803174	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11808099	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11811780	0.80[EUR][1000 genomes]
rs12119232	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12123727	0.82[EUR][1000 genomes]
rs12126566	0.91[ASN][1000 genomes]
rs12127026	0.92[EUR][1000 genomes]
rs12128536	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12132221	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs15655	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16843230	0.97[ASN][1000 genomes]
rs16843251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17649050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17649068	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2298914	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2421911	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3753539	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3766653	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55670848	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58455759	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6656003	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6659874	1.00[CEU][hapmap]
rs6662720	1.00[CEU][hapmap]
rs6667559	1.00[CEU][hapmap]
rs6669263	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6670427	1.00[CEU][hapmap]
rs6678890	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6679027	0.81[YRI][hapmap]
rs6679354	0.92[EUR][1000 genomes]
rs6688823	0.85[YRI][hapmap]
rs7536436	0.92[EUR][1000 genomes]
rs7536543	0.92[EUR][1000 genomes]
rs9662506	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10489249	VAMP4	cis	Temporal Cortex	GTEx
rs10489249	VAMP4	cis	multi-tissue	Pritchard
rs10489249	VAMP4	Cis_1M	lymphoblastoid	RTeQTL
rs10489249	VAMP4	cis	Brain Pons	GTEx
rs10489249	VAMP4	cis	Frontal Cortex	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171712000-171723400	Weak transcription	Lung	lung
2	chr1:171712200-171715800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:171712400-171714600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:171713400-171716200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:171713600-171722200	Weak transcription	NHLF	lung
6	chr1:171713600-171722800	Weak transcription	HMEC	breast
7	chr1:171714000-171714600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr1:171714000-171714800	Enhancers	Primary neutrophils fromperipheralblood	blood

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