Variant report

Variant	rs1019309
Chromosome Location	chr7:12251671-12251672
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:12251263..12253237-chr7:12442665..12444579,2	K562	blood:
2	chr7:12251087..12251775-chr7:12361635..12362202,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146530	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1019306	0.86[ASN][1000 genomes]
rs1019307	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1019308	0.86[ASN][1000 genomes]
rs1020005	0.84[ASN][1000 genomes]
rs1020006	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10234805	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10278257	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10281425	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1042949	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1054168	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1054169	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1060700	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10950391	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10950392	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10950393	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10950394	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10950395	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10950396	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10950397	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10950398	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11509880	0.83[ASN][1000 genomes]
rs11971133	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11974304	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11974335	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11981005	0.81[ASN][1000 genomes]
rs12667950	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12668625	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12669919	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12699323	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12699324	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12699332	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12699333	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12699338	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13229988	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13230513	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13237518	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13237715	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1435524	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1435525	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1435526	0.82[ASN][1000 genomes]
rs1435527	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1435543	0.81[ASN][1000 genomes]
rs1468801	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1468802	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1468803	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1468804	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1548884	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1990620	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1990621	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1990622	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2043539	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2160269	0.81[ASN][1000 genomes]
rs2302633	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2302634	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2302635	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2356065	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28549831	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3173615	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34150432	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3800841	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3800842	0.80[ASN][1000 genomes]
rs3800843	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3800845	0.80[ASN][1000 genomes]
rs3800847	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3807865	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3807866	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3815535	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3823612	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4721056	0.99[ASN][1000 genomes]
rs4721057	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4721058	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4721059	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4721060	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4721061	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4721064	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5011431	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5011432	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5011433	0.81[ASN][1000 genomes]
rs5011434	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5011436	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5011438	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5011439	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6415232	0.85[ASN][1000 genomes]
rs6460895	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6460896	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6460897	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6460898	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6460899	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6460900	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6460901	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6460902	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6460903	0.85[ASN][1000 genomes]
rs6460905	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6460906	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6947327	0.85[ASN][1000 genomes]
rs6948844	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6966757	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6966915	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6974465	0.83[ASN][1000 genomes]
rs7781670	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785087	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7785189	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7791726	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7792410	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7797705	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7804234	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7804433	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7804736	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7805419	0.90[EUR][1000 genomes]
rs7809700	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1021710	chr7:12164993-12251790	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	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
5	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
rs1019309	TMEM106B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12249800-12251800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:12249800-12251800	Active TSS	Brain Cingulate Gyrus	brain
3	chr7:12249800-12251800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr7:12249800-12252000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:12249800-12252200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:12249800-12252200	Active TSS	Right Atrium	heart
7	chr7:12249800-12253000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr7:12250000-12251800	Active TSS	H1 Cell Line	embryonic stem cell
9	chr7:12250000-12251800	Active TSS	H9 Cell Line	embryonic stem cell
10	chr7:12250000-12251800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:12250000-12251800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:12250000-12251800	Active TSS	Aorta	Aorta
13	chr7:12250000-12251800	Active TSS	Brain Hippocampus Middle	brain
14	chr7:12250000-12251800	Active TSS	Fetal Intestine Large	intestine
15	chr7:12250000-12251800	Active TSS	Left Ventricle	heart
16	chr7:12250000-12251800	Active TSS	Ovary	ovary
17	chr7:12250000-12251800	Active TSS	Right Ventricle	heart
18	chr7:12250000-12251800	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr7:12250000-12251800	Active TSS	NHDF-Ad	bronchial
20	chr7:12250000-12251800	Active TSS	NHLF	lung
21	chr7:12250000-12252000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr7:12250000-12252000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:12250000-12252000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr7:12250000-12252000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:12250000-12252000	Active TSS	Colonic Mucosa	Colon
26	chr7:12250000-12252000	Active TSS	Fetal Muscle Trunk	muscle
27	chr7:12250000-12252200	Active TSS	A549	lung
28	chr7:12250000-12252400	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr7:12250200-12251800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr7:12250200-12251800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr7:12250200-12251800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:12250200-12251800	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr7:12250200-12251800	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr7:12250200-12251800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr7:12250200-12251800	Active TSS	Esophagus	oesophagus
36	chr7:12250200-12251800	Active TSS	Gastric	stomach
37	chr7:12250200-12251800	Active TSS	Lung	lung
38	chr7:12250200-12251800	Active TSS	Pancreas	Pancrea
39	chr7:12250200-12251800	Active TSS	Rectal Smooth Muscle	rectum
40	chr7:12250200-12251800	Active TSS	Small Intestine	intestine
41	chr7:12250200-12252000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr7:12250200-12252000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:12250200-12252000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr7:12250200-12252200	Active TSS	Fetal Kidney	kidney
45	chr7:12250400-12251800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr7:12250400-12251800	Active TSS	HMEC	breast
47	chr7:12250400-12252000	Active TSS	HSMM	muscle
48	chr7:12250400-12252200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr7:12250400-12252200	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr7:12250600-12252000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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