Variant report

Variant	rs17102423
Chromosome Location	chr14:65604728-65604729
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10873180	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873181	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873182	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873183	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873185	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11158574	0.85[CEU][hapmap]
rs11158577	0.84[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11158578	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11623603	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11626156	0.88[EUR][1000 genomes]
rs11626496	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11627859	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12100605	0.91[EUR][1000 genomes]
rs12884836	0.84[EUR][1000 genomes]
rs12887607	0.83[CEU][hapmap]
rs17825846	0.88[CEU][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2093989	0.89[ASN][1000 genomes]
rs2898863	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34062462	0.85[EUR][1000 genomes]
rs35002541	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4899161	0.84[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4902362	0.81[EUR][1000 genomes]
rs4902363	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902364	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4902365	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4902367	0.85[EUR][1000 genomes]
rs61987428	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61987429	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7156617	0.84[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs8004805	0.95[CEU][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs8015330	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8018788	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181939	0.82[CEU][hapmap]
rs868814	0.96[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832816	chr14:65473244-65644645	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	esv1833060	chr14:65594460-65607642	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv989058	chr14:65601785-65607798	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv3530651	chr14:65604499-65609897	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv564910	chr14:65604728-65607752	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv564911	chr14:65604728-65607817	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17102423	SIX4	cis	cerebellum	SCAN
rs17102423	MAX	cis	parietal	SCAN
rs17102423	WDR89	cis	cerebellum	SCAN
rs17102423	RAB15	cis	cerebellum	SCAN
rs17102423	GPX2	cis	cerebellum	SCAN
rs17102423	CHRNA5	trans	cerebellum	SCAN
rs17102423	MAX	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65601600-65605400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr14:65604200-65605000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr14:65604400-65604800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr14:65604400-65604800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr14:65604400-65604800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr14:65604400-65604800	Enhancers	Colonic Mucosa	Colon
7	chr14:65604400-65605000	Enhancers	HMEC	breast
8	chr14:65604400-65605000	Enhancers	NHEK	skin
9	chr14:65604400-65605000	Enhancers	Osteobl	bone
10	chr14:65604400-65605200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr14:65604400-65605200	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr14:65604400-65605200	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr14:65604400-65605400	Enhancers	Fetal Intestine Small	intestine
14	chr14:65604600-65604800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr14:65604600-65604800	Enhancers	HSMMtube	muscle
16	chr14:65604600-65605400	Enhancers	Fetal Intestine Large	intestine

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