Variant report

Variant	rs9608798
Chromosome Location	chr22:30016378-30016379
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30007746..30010687-chr22:30014931..30018872,3	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1058642	0.82[ASN][1000 genomes]
rs12172347	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12484392	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13054618	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13055568	0.97[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13055746	0.97[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13057041	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800538	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1807506	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2024116	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024119	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024121	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2267147	0.81[ASN][1000 genomes]
rs2348683	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348684	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34013089	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3940296	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4470427	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67884471	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715490	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7287318	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8142111	0.82[ASN][1000 genomes]
rs867088	0.81[ASN][1000 genomes]
rs9608781	0.82[ASN][1000 genomes]
rs9608785	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608787	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608789	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608790	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608794	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613956	0.82[ASN][1000 genomes]
rs9613957	0.82[ASN][1000 genomes]
rs9613961	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9613963	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9613965	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613970	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613971	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613975	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613977	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613978	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613979	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613980	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9613983	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613984	0.97[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613986	0.97[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613990	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613991	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613992	0.97[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9613993	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613994	0.97[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613995	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9613996	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613997	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9613998	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9613999	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9614004	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614006	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614018	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv817417	chr22:29998464-30035142	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9608798	THOC5	cis	Adipose Subcutaneous	GTEx
rs9608798	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs9608798	THOC5	cis	Thyroid	GTEx
rs9608798	THOC5	cis	Artery Tibial	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30000400-30026600	Weak transcription	Gastric	stomach
2	chr22:30001000-30019400	Weak transcription	Thymus	Thymus
3	chr22:30002000-30017600	Weak transcription	Primary T cells from cord blood	blood
4	chr22:30002800-30017600	Weak transcription	Lung	lung
5	chr22:30003000-30016600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr22:30003400-30017200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr22:30003600-30016400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr22:30003800-30032800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr22:30005200-30019400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr22:30005400-30017800	Weak transcription	Primary B cells from cord blood	blood
11	chr22:30006800-30019000	Weak transcription	Fetal Thymus	thymus
12	chr22:30007400-30016800	Weak transcription	Fetal Muscle Leg	muscle
13	chr22:30007600-30017400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr22:30009600-30017600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr22:30011000-30017800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr22:30011600-30016800	Weak transcription	Esophagus	oesophagus
17	chr22:30011800-30017000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr22:30011800-30017200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr22:30011800-30026200	Weak transcription	Fetal Stomach	stomach
20	chr22:30013000-30017600	Enhancers	HMEC	breast
21	chr22:30013000-30018400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr22:30013200-30017200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr22:30013200-30017800	Enhancers	NHLF	lung
24	chr22:30013400-30017000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr22:30013400-30018000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr22:30013600-30016800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr22:30014000-30017800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr22:30014200-30016800	Weak transcription	Right Atrium	heart
29	chr22:30014200-30017200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr22:30014200-30017600	Weak transcription	Ovary	ovary
31	chr22:30014200-30017800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr22:30014200-30019200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr22:30014200-30019200	Weak transcription	Psoas Muscle	Psoas
34	chr22:30014200-30021800	Weak transcription	Brain Angular Gyrus	brain
35	chr22:30014400-30016800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr22:30014400-30017000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr22:30014400-30017800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr22:30014400-30018000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr22:30014400-30019200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr22:30014600-30017800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr22:30014600-30017800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr22:30014800-30016800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr22:30014800-30017000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr22:30014800-30017400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr22:30014800-30017600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr22:30014800-30017800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr22:30014800-30017800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr22:30014800-30017800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr22:30014800-30017800	Weak transcription	Brain Cingulate Gyrus	brain

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