Variant report

Variant	rs7536543
Chromosome Location	chr1:171666040-171666041
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1001373	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10489249	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10489251	0.93[EUR][1000 genomes]
rs1052676	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10903	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10913489	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10913490	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10913492	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10913507	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913511	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10913514	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10913529	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10913565	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10913582	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10913587	0.93[EUR][1000 genomes]
rs11576221	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11577073	0.93[EUR][1000 genomes]
rs11577197	0.93[EUR][1000 genomes]
rs11577745	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11578179	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11578699	0.93[EUR][1000 genomes]
rs11578723	0.93[EUR][1000 genomes]
rs11579698	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580415	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580522	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11583920	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11590680	0.93[EUR][1000 genomes]
rs11590714	0.93[EUR][1000 genomes]
rs11799420	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11801846	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11803174	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11808099	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11811780	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12118409	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12119232	0.94[EUR][1000 genomes]
rs12119553	0.85[AMR][1000 genomes]
rs12123727	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12125429	0.86[AFR][1000 genomes]
rs12127026	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12128536	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12132221	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs15655	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17649050	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17649068	0.92[EUR][1000 genomes]
rs17649250	1.00[CEU][hapmap]
rs2298914	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2421911	0.89[EUR][1000 genomes]
rs3766653	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55670848	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56091821	0.86[AFR][1000 genomes]
rs58455759	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6656003	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6659874	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6662720	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs6667559	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6669263	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6670427	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[YRI][hapmap]
rs6678890	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6679354	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7528057	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7536436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9659845	1.00[YRI][hapmap]
rs9661596	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9662174	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9662506	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs9662853	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7536543	VAMP4	cis	multi-tissue	Pritchard
rs7536543	VAMP4	cis	Temporal Cortex	GTEx
rs7536543	VAMP4	cis	Frontal Cortex	GTEx
rs7536543	VAMP4	Cis_1M	lymphoblastoid	RTeQTL
rs7536543	VAMP4	cis	Brain Pons	GTEx
rs7536543	VAMP4	cis	Cerebellum	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171664000-171668400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:171664200-171667600	Weak transcription	Left Ventricle	heart
3	chr1:171664400-171685800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:171664600-171674400	Weak transcription	Primary T cells from cord blood	blood
5	chr1:171664800-171668200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:171664800-171684800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:171665000-171669000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:171665000-171692000	Weak transcription	Brain Substantia Nigra	brain
9	chr1:171665400-171674600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:171665600-171705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:171665600-171708800	Weak transcription	Brain Angular Gyrus	brain
12	chr1:171665800-171666400	ZNF genes & repeats	Primary B cells from cord blood	blood
13	chr1:171665800-171666800	Strong transcription	Stomach Smooth Muscle	stomach
14	chr1:171665800-171667400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:171666000-171667600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:171666000-171668200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:171666000-171668400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:171666000-171668400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:171666000-171669000	Strong transcription	Aorta	Aorta
20	chr1:171666000-171674200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:171666000-171676000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:171666000-171676600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:171666000-171685000	Weak transcription	Brain Germinal Matrix	brain
24	chr1:171666000-171705400	Weak transcription	Pancreas	Pancrea

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