Variant report

Variant	rs4470427
Chromosome Location	chr22:29969378-29969379
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	chr22:29968594..29971400-chr22:29974494..29977616,3	MCF-7	breast:
2	chr22:29964781..29966477-chr22:29968407..29970909,2	K562	blood:

Variant related genes	Relation type
ENSG00000184117	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1058642	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11090569	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12161054	0.84[EUR][1000 genomes]
rs12172347	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12484392	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13054618	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13055568	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13055746	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13056992	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13057041	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1800538	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1807506	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2024116	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2024119	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2024121	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072301	0.84[EUR][1000 genomes]
rs2240638	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2267147	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270077	0.84[EUR][1000 genomes]
rs2348672	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2348677	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2348683	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2348684	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2881994	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34013089	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35404981	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3940296	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4479529	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6006178	0.81[EUR][1000 genomes]
rs67292640	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs67884471	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs715490	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7287318	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7292442	0.83[EUR][1000 genomes]
rs737975	0.84[EUR][1000 genomes]
rs737980	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs737981	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs8142111	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs867088	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9608781	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9608785	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9608787	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9608789	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9608790	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9608794	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9608798	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9608799	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9613940	0.84[EUR][1000 genomes]
rs9613942	0.85[EUR][1000 genomes]
rs9613943	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9613956	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9613957	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9613958	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9613961	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9613963	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613965	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9613970	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613971	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613975	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613977	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613978	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9613979	0.85[ASN][1000 genomes]
rs9613983	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613984	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613986	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613990	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613991	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613992	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613993	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613994	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613995	0.81[EUR][1000 genomes]
rs9613996	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613997	0.80[EUR][1000 genomes]
rs9613998	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9613999	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9614004	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9614006	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9614011	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9614014	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9614018	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs999458	0.80[AFR][1000 genomes];0.85[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4470427	THOC5	cis	Thyroid	GTEx
rs4470427	THOC5	cis	Artery Tibial	GTEx
rs4470427	THOC5	cis	Adipose Subcutaneous	GTEx
rs4470427	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29950200-29976000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:29950400-29976200	Weak transcription	HMEC	breast
3	chr22:29950600-29971600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:29950800-29976200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr22:29951200-29971400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr22:29951600-29971600	Strong transcription	Fetal Stomach	stomach
7	chr22:29952000-29976400	Weak transcription	Right Atrium	heart
8	chr22:29955000-29976000	Weak transcription	NHEK	skin
9	chr22:29955400-29976000	Weak transcription	HUVEC	blood vessel
10	chr22:29957400-29976200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr22:29957600-29976200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr22:29958000-29975800	Weak transcription	Stomach Mucosa	stomach
13	chr22:29958400-29976000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr22:29958400-29976200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr22:29958400-29976400	Weak transcription	Primary B cells from cord blood	blood
16	chr22:29958400-29976400	Weak transcription	NHDF-Ad	bronchial
17	chr22:29958600-29976200	Weak transcription	HSMM	muscle
18	chr22:29961000-29975800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr22:29961800-29974600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr22:29962200-29976000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr22:29963600-29976000	Weak transcription	Fetal Brain Male	brain
22	chr22:29963600-29976000	Weak transcription	NH-A	brain
23	chr22:29965200-29976000	Weak transcription	Fetal Kidney	kidney
24	chr22:29965200-29976400	Weak transcription	Fetal Lung	lung
25	chr22:29965400-29970800	Weak transcription	A549	lung
26	chr22:29965400-29975800	Weak transcription	GM12878-XiMat	blood
27	chr22:29965400-29976000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr22:29965400-29976200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr22:29965400-29976200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr22:29965400-29976200	Weak transcription	Adipose Nuclei	Adipose
31	chr22:29965400-29976200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr22:29965400-29976200	Weak transcription	Colonic Mucosa	Colon
33	chr22:29965400-29976400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr22:29965400-29976400	Weak transcription	HSMMtube	muscle
35	chr22:29965600-29976200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr22:29965800-29976000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr22:29965800-29976200	Weak transcription	Placenta	Placenta
38	chr22:29965800-29976400	Weak transcription	Brain Angular Gyrus	brain
39	chr22:29966000-29974400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr22:29966200-29975800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr22:29966200-29976200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr22:29966200-29976200	Weak transcription	Right Ventricle	heart
43	chr22:29966400-29974400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr22:29966400-29974600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr22:29966400-29975600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr22:29966400-29975600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr22:29966400-29976000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr22:29966400-29976000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr22:29966400-29976000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr22:29966400-29976000	Weak transcription	NHLF	lung

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