Variant report

Variant	rs9614005
Chromosome Location	chr22:30002603-30002604
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1058642	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11090569	0.81[EUR][1000 genomes]
rs12172347	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12484392	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13054618	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13055568	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13055746	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13056992	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13057041	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800538	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1807506	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2024116	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024119	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024121	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2072301	0.96[CEU][hapmap]
rs2240638	0.95[CEU][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs2245185	0.87[LWK][hapmap]
rs2267147	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2348672	0.80[EUR][1000 genomes]
rs2348677	0.80[EUR][1000 genomes]
rs2348683	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348684	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530670	0.88[LWK][hapmap]
rs34013089	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35404981	0.80[EUR][1000 genomes]
rs3940296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4470427	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67292640	0.81[EUR][1000 genomes]
rs67884471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7287318	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs737975	0.96[CEU][hapmap]
rs737980	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs737981	0.80[EUR][1000 genomes]
rs8142111	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs867088	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9608781	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9608785	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608787	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608789	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608798	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608799	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613940	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs9613942	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs9613943	0.80[EUR][1000 genomes]
rs9613956	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613957	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613958	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9613961	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9613963	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9613965	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613977	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613978	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613979	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613980	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9613983	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613986	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613990	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613991	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613992	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9613993	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613994	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613995	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9613996	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613997	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9613998	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9613999	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9614004	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614014	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999458	0.82[JPT][hapmap];0.85[YRI][hapmap];0.80[EUR][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9614005	THOC5	cis	Adipose Subcutaneous	GTEx
rs9614005	NF2	cis	parietal	SCAN
rs9614005	NIPSNAP1	cis	parietal	SCAN
rs9614005	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs9614005	NIPSNAP1	cis	lymphoblastoid	seeQTL
rs9614005	THOC5	cis	Artery Tibial	GTEx
rs9614005	THOC5	cis	Thyroid	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30000400-30002800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr22:30000400-30003000	Enhancers	Pancreas	Pancrea
3	chr22:30000400-30026600	Weak transcription	Gastric	stomach
4	chr22:30000600-30002800	Enhancers	Placenta	Placenta
5	chr22:30000800-30002800	Enhancers	Left Ventricle	heart
6	chr22:30000800-30002800	Enhancers	Lung	lung
7	chr22:30001000-30002800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr22:30001000-30004800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr22:30001000-30013400	Weak transcription	Fetal Kidney	kidney
10	chr22:30001000-30019400	Weak transcription	Thymus	Thymus
11	chr22:30001200-30002800	Enhancers	HepG2	liver
12	chr22:30001200-30004600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:30001200-30005400	Weak transcription	Aorta	Aorta
14	chr22:30001200-30006600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr22:30001200-30013800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr22:30001400-30003400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr22:30001400-30003600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr22:30001400-30003600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr22:30001400-30003800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr22:30001400-30004800	Weak transcription	Primary B cells from cord blood	blood
21	chr22:30001400-30005200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr22:30001400-30005800	Weak transcription	Fetal Intestine Large	intestine
23	chr22:30001400-30006600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr22:30001400-30013400	Weak transcription	Brain Angular Gyrus	brain
25	chr22:30001400-30013400	Weak transcription	Ovary	ovary
26	chr22:30001400-30013400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr22:30001400-30014000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr22:30001600-30002800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr22:30001600-30003000	Enhancers	Primary T cells fromperipheralblood	blood
30	chr22:30001600-30005000	Weak transcription	K562	blood
31	chr22:30001600-30005400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr22:30001600-30006400	Weak transcription	Liver	Liver
33	chr22:30001600-30013400	Weak transcription	Fetal Lung	lung
34	chr22:30001600-30013600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr22:30001800-30002800	Enhancers	GM12878-XiMat	blood
36	chr22:30001800-30003000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr22:30001800-30003000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr22:30001800-30003800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr22:30002000-30003000	Strong transcription	Fetal Stomach	stomach
40	chr22:30002000-30003000	Weak transcription	Osteobl	bone
41	chr22:30002000-30003200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr22:30002000-30003200	Genic enhancers	A549	lung
43	chr22:30002000-30003400	Enhancers	Right Atrium	heart
44	chr22:30002000-30003600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr22:30002000-30003600	Enhancers	NH-A	brain
46	chr22:30002000-30004600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr22:30002000-30004800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr22:30002000-30005400	Weak transcription	Brain Germinal Matrix	brain
49	chr22:30002000-30005600	Enhancers	HUVEC	blood vessel
50	chr22:30002000-30006000	Weak transcription	Fetal Thymus	thymus

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