Variant report

Variant	rs67292640
Chromosome Location	chr22:29947666-29947667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29939607..29941990-chr22:29945256..29947722,2	MCF-7	breast:
2	chr22:29938209..29940408-chr22:29946980..29949798,2	K562	blood:
3	chr22:29947295..29951735-chr22:29976015..29980297,4	K562	blood:

Variant related genes	Relation type
ENSG00000184117	Chromatin interaction
ENSG00000100296	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1058642	0.95[EUR][1000 genomes]
rs11090569	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12161054	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12484392	0.82[EUR][1000 genomes]
rs13055568	0.83[EUR][1000 genomes]
rs13055746	0.83[EUR][1000 genomes]
rs13056992	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs13057041	0.82[EUR][1000 genomes]
rs1800538	0.82[EUR][1000 genomes]
rs1807506	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2024116	0.83[EUR][1000 genomes]
rs2024119	0.83[EUR][1000 genomes]
rs2024121	0.80[EUR][1000 genomes]
rs2072301	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240638	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267147	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2270077	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2348672	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2348677	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2348683	0.81[EUR][1000 genomes]
rs2881994	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34013089	0.83[EUR][1000 genomes]
rs35404981	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4470427	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4479529	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6006178	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67884471	0.81[EUR][1000 genomes]
rs715490	0.80[EUR][1000 genomes]
rs7292442	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737975	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737980	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs737981	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8142111	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs867088	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9608781	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9608785	0.83[EUR][1000 genomes]
rs9608787	0.81[EUR][1000 genomes]
rs9608789	0.81[EUR][1000 genomes]
rs9608790	0.81[EUR][1000 genomes]
rs9613940	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9613942	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9613943	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9613956	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9613957	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9613958	0.90[EUR][1000 genomes]
rs9613961	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9613963	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9613965	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9613970	0.83[EUR][1000 genomes]
rs9613971	0.83[EUR][1000 genomes]
rs9613975	0.83[EUR][1000 genomes]
rs9613977	0.83[EUR][1000 genomes]
rs9613978	0.83[EUR][1000 genomes]
rs9613983	0.82[EUR][1000 genomes]
rs9613984	0.83[EUR][1000 genomes]
rs9613986	0.81[EUR][1000 genomes]
rs9613990	0.81[EUR][1000 genomes]
rs9613991	0.81[EUR][1000 genomes]
rs9613992	0.81[EUR][1000 genomes]
rs9613993	0.80[EUR][1000 genomes]
rs9613994	0.81[EUR][1000 genomes]
rs9613996	0.81[EUR][1000 genomes]
rs9613998	0.80[EUR][1000 genomes]
rs9613999	0.80[EUR][1000 genomes]
rs9614004	0.81[EUR][1000 genomes]
rs9614006	0.81[EUR][1000 genomes]
rs999458	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs67292640	THOC5	cis	Thyroid	GTEx
rs67292640	THOC5	cis	Adipose Subcutaneous	GTEx
rs67292640	THOC5	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29900400-29949200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:29902600-29949000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr22:29910000-29947800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr22:29910600-29947800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr22:29913600-29949200	Weak transcription	Right Atrium	heart
6	chr22:29918000-29948000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr22:29925000-29949200	Weak transcription	Small Intestine	intestine
8	chr22:29925800-29948800	Weak transcription	Stomach Mucosa	stomach
9	chr22:29930200-29948800	Weak transcription	Fetal Heart	heart
10	chr22:29930600-29947800	Strong transcription	Fetal Intestine Small	intestine
11	chr22:29930600-29947800	Strong transcription	Fetal Stomach	stomach
12	chr22:29930800-29947800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr22:29933000-29949000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr22:29933200-29949000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr22:29935800-29948600	Weak transcription	Fetal Brain Male	brain
16	chr22:29939600-29949200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr22:29940800-29949000	Weak transcription	NHDF-Ad	bronchial
18	chr22:29940800-29949200	Weak transcription	Psoas Muscle	Psoas
19	chr22:29943000-29948000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr22:29944800-29949200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr22:29944800-29949200	Weak transcription	Colon Smooth Muscle	Colon
22	chr22:29945000-29948800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr22:29945000-29948800	Weak transcription	NHEK	skin
24	chr22:29945000-29949000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr22:29945000-29949200	Weak transcription	Ovary	ovary
26	chr22:29945000-29949200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr22:29945200-29948600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr22:29945200-29948600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr22:29945200-29948600	Weak transcription	Right Ventricle	heart
30	chr22:29945200-29948800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr22:29945200-29948800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr22:29945200-29948800	Weak transcription	Adipose Nuclei	Adipose
33	chr22:29945200-29948800	Weak transcription	Esophagus	oesophagus
34	chr22:29945200-29948800	Weak transcription	Placenta	Placenta
35	chr22:29945200-29948800	Weak transcription	HMEC	breast
36	chr22:29945200-29949000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr22:29945200-29949000	Weak transcription	Colonic Mucosa	Colon
38	chr22:29945200-29949200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr22:29945200-29949200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr22:29945200-29949200	Weak transcription	Brain Substantia Nigra	brain
41	chr22:29945200-29949200	Weak transcription	Pancreas	Pancrea
42	chr22:29945400-29948600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr22:29945400-29948600	Weak transcription	Liver	Liver
44	chr22:29945400-29948800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr22:29945400-29948800	Weak transcription	Brain Anterior Caudate	brain
46	chr22:29945400-29948800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr22:29945400-29949000	Weak transcription	Fetal Intestine Large	intestine
48	chr22:29945400-29949200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr22:29945400-29949200	Weak transcription	Left Ventricle	heart
50	chr22:29945400-29949200	Weak transcription	Lung	lung

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