Variant report

Variant	rs16843251
Chromosome Location	chr1:171725830-171725831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr1:171725337-171725842	K562	blood:	n/a	n/a
2	RCOR1	chr1:171725276-171726042	K562	blood:	n/a	n/a
3	CCNT2	chr1:171725494-171725874	K562	blood:	n/a	n/a
4	TAL1	chr1:171725466-171726097	K562	blood:	n/a	chr1:171725679-171725694
5	KAP1	chr1:171725790-171726628	K562	blood:	n/a	n/a
6	RCOR1	chr1:171725442-171725904	K562	blood:	n/a	n/a
7	POLR2A	chr1:171722769-171728047	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:171724145..171725831-chr1:171749285..171750823,2	K562	blood:
2	chr1:171709554..171712819-chr1:171724332..171729197,5	K562	blood:
3	chr1:171709658..171712904-chr1:171725619..171729545,3	MCF-7	breast:
4	chr1:171722184..171727474-chr1:171729363..171734018,7	K562	blood:
5	chr1:171723775..171729031-chr1:171729363..171735304,8	K562	blood:
6	chr1:171719571..171721308-chr1:171725110..171727162,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000232261	TF binding region
ENSG00000271459	TF binding region
ENSG00000010165	Chromatin interaction
ENSG00000117533	Chromatin interaction
ENSG00000236741	Chromatin interaction
ENSG00000232261	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1001373	0.81[GIH][hapmap];0.83[JPT][hapmap]
rs10489249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10489251	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10753181	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798603	0.86[YRI][hapmap]
rs10913507	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10913529	0.81[GIH][hapmap];0.83[JPT][hapmap]
rs10913530	0.86[YRI][hapmap]
rs10913565	0.83[JPT][hapmap]
rs10913578	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913582	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913587	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11577073	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11577197	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11577745	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11578699	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11578723	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11580522	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11583920	0.83[JPT][hapmap]
rs11590680	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11590714	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12096984	0.90[YRI][hapmap]
rs12119232	0.92[ASN][1000 genomes]
rs12120152	0.86[YRI][hapmap]
rs12126566	0.91[ASN][1000 genomes]
rs15655	0.81[GIH][hapmap]
rs16843230	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17649050	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17649068	0.97[ASN][1000 genomes]
rs17649250	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2073484	0.86[YRI][hapmap]
rs2227229	0.90[YRI][hapmap]
rs2298914	0.83[JPT][hapmap]
rs2421911	0.91[ASN][1000 genomes]
rs3753539	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4342884	0.82[YRI][hapmap]
rs4468194	0.86[YRI][hapmap]
rs6665581	0.86[YRI][hapmap]
rs6670427	0.83[CEU][hapmap]
rs6672082	0.85[YRI][hapmap]
rs6673782	0.89[YRI][hapmap]
rs6674688	0.90[YRI][hapmap]
rs6688447	0.83[YRI][hapmap]
rs6700606	0.86[YRI][hapmap]
rs999685	0.86[YRI][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16843251	VAMP4	cis	multi-tissue	Pritchard
rs16843251	DCAF6	cis	cerebellum	SCAN
rs16843251	VAMP4	cis	Brain Pons	GTEx
rs16843251	DNM3	cis	cerebellum	SCAN
rs16843251	VAMP4	cis	lymphoblastoid	seeQTL
rs16843251	VAMP4	cis	Frontal Cortex	GTEx
rs16843251	METTL13	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171723600-171730200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:171724200-171727400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:171724200-171731400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:171724400-171726400	Weak transcription	Fetal Heart	heart
5	chr1:171724400-171726400	Weak transcription	NHEK	skin
6	chr1:171724400-171727400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:171724400-171729600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:171724600-171726800	Enhancers	K562	blood

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