Variant report

Variant	rs12666279
Chromosome Location	chr7:12260552-12260553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:12260062..12264264-chr7:12265480..12268188,5	K562	blood:
2	chr7:12256580..12259981-chr7:12260401..12263217,3	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10488192	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11983898	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12673866	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16877363	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17165702	0.84[ASN][1000 genomes]
rs58759116	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62435687	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62435691	0.98[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62435714	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6967026	0.81[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12666279	TMEM106B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12252000-12261200	Weak transcription	Aorta	Aorta
2	chr7:12252000-12261200	Weak transcription	Esophagus	oesophagus
3	chr7:12252000-12261200	Weak transcription	Stomach Mucosa	stomach
4	chr7:12252000-12263600	Weak transcription	Thymus	Thymus
5	chr7:12252000-12266200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:12252000-12271000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:12252000-12271600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:12252000-12277600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:12252000-12278200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:12252000-12280000	Weak transcription	Colonic Mucosa	Colon
11	chr7:12252000-12280000	Weak transcription	Right Ventricle	heart
12	chr7:12252000-12285400	Weak transcription	Spleen	Spleen
13	chr7:12252200-12262200	Weak transcription	GM12878-XiMat	blood
14	chr7:12252200-12263600	Weak transcription	NH-A	brain
15	chr7:12252200-12263800	Weak transcription	Osteobl	bone
16	chr7:12252200-12279200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:12252200-12279400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:12252400-12261200	Weak transcription	Pancreas	Pancrea
19	chr7:12252400-12262200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr7:12252400-12263200	Weak transcription	Left Ventricle	heart
21	chr7:12252400-12263400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:12252400-12265800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr7:12252400-12266000	Weak transcription	Small Intestine	intestine
24	chr7:12252400-12269400	Weak transcription	HUVEC	blood vessel
25	chr7:12252400-12271200	Weak transcription	K562	blood
26	chr7:12252400-12271400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr7:12252400-12272600	Weak transcription	Gastric	stomach
28	chr7:12252400-12277200	Weak transcription	Fetal Brain Male	brain
29	chr7:12252400-12278600	Weak transcription	NHEK	skin
30	chr7:12252400-12281600	Weak transcription	HSMMtube	muscle
31	chr7:12252400-12284000	Weak transcription	Fetal Intestine Small	intestine
32	chr7:12252600-12264000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:12252600-12271000	Weak transcription	Fetal Heart	heart
34	chr7:12252600-12278200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr7:12252600-12279600	Weak transcription	Brain Angular Gyrus	brain
36	chr7:12252800-12272600	Weak transcription	Hela-S3	cervix
37	chr7:12252800-12279000	Weak transcription	Brain Substantia Nigra	brain
38	chr7:12253200-12272400	Weak transcription	HepG2	liver
39	chr7:12253400-12261200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr7:12254000-12260600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr7:12254000-12261000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:12254000-12261200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr7:12254000-12279400	Strong transcription	Placenta	Placenta
44	chr7:12254200-12261000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr7:12254400-12261000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr7:12254400-12264600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr7:12254600-12260600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr7:12254600-12260800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr7:12254600-12262200	Strong transcription	Fetal Thymus	thymus
50	chr7:12254800-12260800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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