Variant report

Variant	rs17541464
Chromosome Location	chr7:12462675-12462676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10229433	0.88[ASN][1000 genomes]
rs10251962	1.00[JPT][hapmap]
rs10267801	0.84[EUR][1000 genomes]
rs10270435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10271597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10273416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10276545	0.84[ASN][1000 genomes]
rs11971590	1.00[JPT][hapmap]
rs1371607	0.96[AFR][1000 genomes]
rs1595800	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs1595802	0.84[EUR][1000 genomes]
rs17443848	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17444044	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17444141	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17444203	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444259	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17541242	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28566049	0.86[ASN][1000 genomes]
rs57550598	0.84[ASN][1000 genomes]
rs58205663	0.84[ASN][1000 genomes]
rs62448593	0.83[EUR][1000 genomes]
rs62448594	0.83[EUR][1000 genomes]
rs62448596	0.84[EUR][1000 genomes]
rs62448597	0.83[EUR][1000 genomes]
rs62448600	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62448602	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62448619	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62448620	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62448621	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62448622	0.92[AFR][1000 genomes]
rs62448623	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6460938	0.83[CEU][hapmap]
rs6945067	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs6966791	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs6968277	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6968695	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs7802454	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7809263	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs954660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv887635	chr7:12410112-12474635	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv887636	chr7:12424405-12498138	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv464375	chr7:12428803-12505373	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv606226	chr7:12428803-12505373	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
13	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
14	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
15	nsv516511	chr7:12439672-12479584	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
16	nsv887639	chr7:12448482-12488535	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17541464	TMEM106B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12458800-12463200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:12461000-12463400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr7:12461200-12463400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr7:12461400-12462800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr7:12461400-12463400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr7:12461400-12463400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:12461400-12463800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:12461600-12463000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr7:12461600-12463200	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr7:12461600-12463600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:12461600-12464000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:12461600-12464200	Enhancers	HMEC	breast
13	chr7:12461800-12464000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:12461800-12464000	Enhancers	HUVEC	blood vessel
15	chr7:12462000-12463400	Enhancers	Osteobl	bone
16	chr7:12462200-12462800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:12462200-12463400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr7:12462200-12463600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:12462200-12463800	Enhancers	H9 Cell Line	embryonic stem cell
20	chr7:12462400-12463000	Flanking Active TSS	A549	lung
21	chr7:12462400-12463400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr7:12462400-12463800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr7:12462400-12463800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr7:12462400-12463800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr7:12462400-12463800	Enhancers	HSMM	muscle
26	chr7:12462400-12463800	Enhancers	NHEK	skin
27	chr7:12462400-12464000	Enhancers	Hela-S3	cervix
28	chr7:12462400-12464000	Enhancers	NHDF-Ad	bronchial
29	chr7:12462400-12464200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:12462400-12464200	Enhancers	NH-A	brain
31	chr7:12462600-12462800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr7:12462600-12463000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:12462600-12463200	Enhancers	NHLF	lung
34	chr7:12462600-12463800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr7:12462600-12463800	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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