Variant report

Variant	rs9613990
Chromosome Location	chr22:29993275-29993276
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29991169..29993450-chr22:30000929..30002699,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1058642	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11090569	0.81[EUR][1000 genomes]
rs12172347	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12484392	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13054618	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13055568	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13055746	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13056992	0.85[EUR][1000 genomes]
rs13057041	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1800538	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1807506	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2024116	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024119	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024121	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240638	0.81[EUR][1000 genomes]
rs2267147	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2348677	0.80[EUR][1000 genomes]
rs2348683	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2348684	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34013089	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3940296	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4470427	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67292640	0.81[EUR][1000 genomes]
rs67884471	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs715490	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7287318	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8142111	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs867088	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9608781	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9608785	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608787	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608789	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608790	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608794	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608798	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608799	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613956	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9613957	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9613958	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613961	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613963	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9613965	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9613970	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613971	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613975	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613977	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613978	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613979	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613980	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9613983	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9613984	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613986	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613991	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613992	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9613993	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613994	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613995	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9613996	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613997	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9613998	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9613999	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614004	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9614006	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9614011	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9614014	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9614018	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9613990	THOC5	cis	Artery Tibial	GTEx
rs9613990	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs9613990	THOC5	cis	Thyroid	GTEx
rs9613990	THOC5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29977600-29998800	Weak transcription	Right Atrium	heart
2	chr22:29977800-29994200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:29985200-29999000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr22:29985200-29999000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr22:29990200-29999000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:29992600-29994200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
7	chr22:29992800-29993400	Active TSS	Brain Anterior Caudate	brain
8	chr22:29992800-29993600	Active TSS	Primary T cells from cord blood	blood
9	chr22:29992800-29993600	Active TSS	Primary T cells fromperipheralblood	blood
10	chr22:29992800-29993600	Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr22:29992800-29993600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr22:29992800-29993600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr22:29992800-29993600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr22:29992800-29993600	Active TSS	Brain Hippocampus Middle	brain
15	chr22:29992800-29993600	Active TSS	Ovary	ovary
16	chr22:29992800-29993600	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr22:29992800-29993600	Active TSS	Rectal Smooth Muscle	rectum
18	chr22:29992800-29999000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr22:29993000-29993400	Active TSS	Primary B cells from cord blood	blood
20	chr22:29993000-29993400	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr22:29993000-29993400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr22:29993000-29993400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr22:29993000-29993400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr22:29993000-29993400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr22:29993000-29993400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr22:29993000-29993400	Active TSS	Fetal Intestine Large	intestine
27	chr22:29993000-29993400	Active TSS	Fetal Muscle Leg	muscle
28	chr22:29993000-29993400	Active TSS	Psoas Muscle	Psoas
29	chr22:29993000-29993400	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr22:29993000-29993400	Active TSS	Thymus	Thymus
31	chr22:29993000-29993400	Active TSS	HSMMtube	muscle
32	chr22:29993000-29993600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr22:29993000-29993600	Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr22:29993000-29993600	Active TSS	Primary B cells from peripheral blood	blood
35	chr22:29993000-29993600	Active TSS	Muscle Satellite Cultured Cells	--
36	chr22:29993000-29993600	Active TSS	Duodenum Mucosa	Duodenum
37	chr22:29993000-29993600	Active TSS	Fetal Kidney	kidney
38	chr22:29993000-29993600	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr22:29993000-29993600	Active TSS	Stomach Smooth Muscle	stomach
40	chr22:29993000-29993800	Active TSS	Adipose Nuclei	Adipose
41	chr22:29993200-29993600	Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr22:29993200-29993600	Active TSS	Liver	Liver
43	chr22:29993200-29993600	Active TSS	Colonic Mucosa	Colon
44	chr22:29993200-29993600	Active TSS	Placenta	Placenta
45	chr22:29993200-29993600	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr22:29993200-29993600	Bivalent/Poised TSS	HepG2	liver
47	chr22:29993200-29994000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr22:29993200-29994000	Active TSS	Monocytes-CD14+_RO01746	blood
49	chr22:29993200-29997800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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