Variant report

Variant	rs10488158
Chromosome Location	chr7:12508894-12508895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10267801	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10273045	1.00[ASN][1000 genomes]
rs10276171	1.00[ASN][1000 genomes]
rs12699381	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12699388	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs12699391	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12699392	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13221702	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13235488	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13245635	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13247370	1.00[ASN][1000 genomes]
rs1595800	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595802	0.94[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17191008	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17274870	1.00[ASN][1000 genomes]
rs17277369	1.00[ASN][1000 genomes]
rs17444044	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444141	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17448913	1.00[ASN][1000 genomes]
rs17541242	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17544637	1.00[ASN][1000 genomes]
rs1866650	1.00[ASN][1000 genomes]
rs2033871	0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs2053378	1.00[ASN][1000 genomes]
rs2053381	0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs2053382	0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs28366613	1.00[ASN][1000 genomes]
rs34644264	1.00[ASN][1000 genomes]
rs34868445	1.00[ASN][1000 genomes]
rs34915661	1.00[ASN][1000 genomes]
rs35589221	1.00[ASN][1000 genomes]
rs4719315	1.00[ASN][1000 genomes]
rs4721105	1.00[ASN][1000 genomes]
rs4721106	1.00[ASN][1000 genomes]
rs4721107	1.00[ASN][1000 genomes]
rs4721108	1.00[ASN][1000 genomes]
rs62447638	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62447639	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62447640	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62447641	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62447642	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448293	1.00[ASN][1000 genomes]
rs62448562	1.00[ASN][1000 genomes]
rs62448563	1.00[ASN][1000 genomes]
rs62448566	1.00[ASN][1000 genomes]
rs62448568	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62448593	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448594	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448596	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448597	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448600	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448602	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448619	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448620	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448621	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62448623	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62449509	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6460935	1.00[ASN][1000 genomes]
rs6460936	1.00[ASN][1000 genomes]
rs6460938	1.00[ASN][1000 genomes]
rs6460942	0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs6944134	1.00[ASN][1000 genomes]
rs6944517	1.00[ASN][1000 genomes]
rs6945067	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948314	1.00[ASN][1000 genomes]
rs6948654	1.00[ASN][1000 genomes]
rs6961238	1.00[ASN][1000 genomes]
rs6966791	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6968664	1.00[ASN][1000 genomes]
rs6968695	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969309	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6970095	1.00[ASN][1000 genomes]
rs6977059	1.00[ASN][1000 genomes]
rs7791634	1.00[ASN][1000 genomes]
rs7796485	1.00[ASN][1000 genomes]
rs7802454	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7808537	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7809263	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811374	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv464373	chr7:12406826-12536336	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv606224	chr7:12406826-12536336	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv887637	chr7:12424405-12508894	Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv887638	chr7:12424405-12519212	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv464376	chr7:12429488-12526282	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv606227	chr7:12429488-12526282	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	esv1801371	chr7:12498138-12522283	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	esv2757212	chr7:12505613-12596535	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv2759511	chr7:12505613-12596535	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10488158	TMEM106B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12504000-12510600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:12508800-12509200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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