Variant report

Variant	rs10028343
Chromosome Location	chr4:119138539-119138540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10001247	0.95[EUR][1000 genomes]
rs10001520	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10004607	0.95[EUR][1000 genomes]
rs10007918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10012051	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10014402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10019969	0.95[EUR][1000 genomes]
rs10020944	0.95[EUR][1000 genomes]
rs10021970	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10023656	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10024765	0.85[EUR][1000 genomes]
rs10028980	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10518291	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11930405	0.95[EUR][1000 genomes]
rs11931778	0.95[EUR][1000 genomes]
rs11931869	0.87[EUR][1000 genomes]
rs11934128	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11934324	1.00[EUR][1000 genomes]
rs11935016	1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11942654	0.85[EUR][1000 genomes]
rs11944236	1.00[EUR][1000 genomes]
rs11945958	1.00[EUR][1000 genomes]
rs11946833	1.00[EUR][1000 genomes]
rs11946941	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11947911	0.95[EUR][1000 genomes]
rs13434652	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13434825	1.00[EUR][1000 genomes]
rs1589719	1.00[EUR][1000 genomes]
rs17049622	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17049625	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17049650	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049676	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049690	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17049693	1.00[EUR][1000 genomes]
rs17049694	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049695	1.00[EUR][1000 genomes]
rs17049697	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049698	1.00[EUR][1000 genomes]
rs17049699	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17049700	1.00[EUR][1000 genomes]
rs17049706	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049718	0.87[EUR][1000 genomes]
rs17693234	1.00[YRI][hapmap]
rs1829910	1.00[EUR][1000 genomes]
rs1829911	1.00[EUR][1000 genomes]
rs2292598	1.00[YRI][hapmap]
rs28374287	1.00[EUR][1000 genomes]
rs28507199	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28515963	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28536042	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28562324	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28589481	1.00[EUR][1000 genomes]
rs28648504	1.00[EUR][1000 genomes]
rs28665669	0.90[EUR][1000 genomes]
rs28667401	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28668316	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28683619	0.86[EUR][1000 genomes]
rs28690846	1.00[EUR][1000 genomes]
rs28734874	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28826087	0.85[EUR][1000 genomes]
rs28848859	0.95[EUR][1000 genomes]
rs28851582	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28856120	0.95[EUR][1000 genomes]
rs28882407	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3805191	1.00[YRI][hapmap]
rs41278063	1.00[EUR][1000 genomes]
rs41278065	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4147036	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4147037	1.00[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs4147038	1.00[EUR][1000 genomes]
rs4147039	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4147040	1.00[EUR][1000 genomes]
rs41520948	1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4557347	0.95[EUR][1000 genomes]
rs60958074	1.00[EUR][1000 genomes]
rs61390934	0.95[EUR][1000 genomes]
rs6824418	1.00[EUR][1000 genomes]
rs6842491	0.95[EUR][1000 genomes]
rs6845921	0.87[EUR][1000 genomes]
rs6848301	0.95[EUR][1000 genomes]
rs6856765	1.00[EUR][1000 genomes]
rs72919205	1.00[EUR][1000 genomes]
rs72919235	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919237	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919245	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919247	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919251	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919254	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919259	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919264	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919267	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919272	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919275	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919276	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919279	0.95[EUR][1000 genomes]
rs7654652	0.95[EUR][1000 genomes]
rs9968544	0.95[EUR][1000 genomes]
rs9992747	0.95[EUR][1000 genomes]
rs9998199	0.95[EUR][1000 genomes]
rs9998981	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9999336	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1009076	chr4:118949490-119269424	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1001236	chr4:118949490-119271243	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv1008236	chr4:118989467-119154024	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv34038	chr4:119035124-119455391	Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1001138	chr4:119095147-119461837	Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv537230	chr4:119095147-119461837	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv4485	chr4:119103349-119144334	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv1002771	chr4:119125361-119571237	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv1003731	chr4:119138262-119506032	Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10028343	SNX7	trans	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119133000-119138600	Strong transcription	Dnd41	blood
2	chr4:119137200-119142200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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