Variant report

Variant	rs6969722
Chromosome Location	chr7:12278437-12278438
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1020004	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10235395	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10236369	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11974384	0.94[EUR][1000 genomes]
rs11983898	0.88[ASN][1000 genomes]
rs12666249	0.87[CEU][hapmap];0.93[GIH][hapmap];0.94[EUR][1000 genomes]
rs12699335	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12699336	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs14978	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1548885	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17149894	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2043538	0.87[EUR][1000 genomes]
rs2043540	0.87[ASN][1000 genomes]
rs2160267	0.93[ASN][1000 genomes]
rs2302632	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4424141	0.96[ASN][1000 genomes]
rs5011432	0.84[ASW][hapmap]
rs6460894	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6966602	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6967026	0.93[ASN][1000 genomes]
rs929637	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.96[ASN][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
rs6969722	TMEM106B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12252000-12280000	Weak transcription	Colonic Mucosa	Colon
2	chr7:12252000-12280000	Weak transcription	Right Ventricle	heart
3	chr7:12252000-12285400	Weak transcription	Spleen	Spleen
4	chr7:12252200-12279200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:12252200-12279400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:12252400-12278600	Weak transcription	NHEK	skin
7	chr7:12252400-12281600	Weak transcription	HSMMtube	muscle
8	chr7:12252400-12284000	Weak transcription	Fetal Intestine Small	intestine
9	chr7:12252600-12279600	Weak transcription	Brain Angular Gyrus	brain
10	chr7:12252800-12279000	Weak transcription	Brain Substantia Nigra	brain
11	chr7:12254000-12279400	Strong transcription	Placenta	Placenta
12	chr7:12255200-12279000	Strong transcription	Liver	Liver
13	chr7:12256400-12279400	Weak transcription	Psoas Muscle	Psoas
14	chr7:12256600-12279600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:12259000-12278800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr7:12259800-12283600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr7:12260400-12279400	Weak transcription	NHDF-Ad	bronchial
18	chr7:12263200-12279400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr7:12264200-12279800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:12264200-12280000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:12264200-12280000	Weak transcription	Ovary	ovary
22	chr7:12264400-12279400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr7:12264600-12279600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr7:12264600-12279600	Weak transcription	Fetal Thymus	thymus
25	chr7:12264600-12279800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr7:12266400-12279400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:12266400-12279600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr7:12266400-12279800	Weak transcription	Small Intestine	intestine
29	chr7:12267000-12279000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr7:12270000-12284400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:12270200-12279000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr7:12270200-12279600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr7:12271600-12278600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr7:12271800-12279600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr7:12271800-12280000	Weak transcription	Osteobl	bone
36	chr7:12271800-12289000	Weak transcription	HSMM	muscle
37	chr7:12272000-12278600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr7:12272000-12278800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr7:12272000-12279200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr7:12272200-12279600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr7:12272400-12280000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr7:12274600-12278800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr7:12274600-12279200	Weak transcription	Primary B cells from cord blood	blood
44	chr7:12274800-12280000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr7:12277000-12278600	Strong transcription	Primary T cells from cord blood	blood
46	chr7:12277000-12278600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr7:12277000-12278600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr7:12277000-12278800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr7:12277000-12278800	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr7:12277000-12279200	Strong transcription	Duodenum Smooth Muscle	Duodenum

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