Variant report

Variant	rs7324458
Chromosome Location	chr13:52708773-52708774
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 129 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1004576	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs1055062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1060631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1134727	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11620583	0.87[CHB][hapmap]
rs12146904	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[ASN][1000 genomes]
rs12431310	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs12560598	0.90[ASN][1000 genomes]
rs1327323	0.87[MEX][hapmap]
rs1571189	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1801243	0.91[CHB][hapmap]
rs1886538	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs1886539	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1886542	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1886543	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886545	0.91[ASN][1000 genomes]
rs1886546	0.90[ASN][1000 genomes]
rs1886547	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1924611	0.86[CHB][hapmap]
rs2004866	0.91[CHB][hapmap]
rs2005182	0.97[ASN][1000 genomes]
rs2181891	0.91[CHB][hapmap]
rs2274202	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2277448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2296347	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];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296348	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2296349	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408544	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408546	0.94[ASN][1000 genomes]
rs2408547	0.95[ASN][1000 genomes]
rs2408548	0.95[ASN][1000 genomes]
rs2408550	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408551	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2408552	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.92[ASN][1000 genomes]
rs2408554	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2408609	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408611	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2897964	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2897965	0.94[ASN][1000 genomes]
rs2897977	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3368	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3742289	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3742291	0.90[ASN][1000 genomes]
rs3783242	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[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818422	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[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825528	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs4261421	0.94[ASN][1000 genomes]
rs4264295	0.94[ASN][1000 genomes]
rs4297592	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs4497567	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4941727	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4943060	0.89[ASN][1000 genomes]
rs61958804	0.91[ASN][1000 genomes]
rs61958805	0.88[ASN][1000 genomes]
rs6561656	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6561658	0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs6650384	0.95[ASN][1000 genomes]
rs6650385	0.95[ASN][1000 genomes]
rs66849828	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7318287	0.94[ASN][1000 genomes]
rs7319784	0.88[ASN][1000 genomes]
rs7320252	0.95[ASN][1000 genomes]
rs7320429	0.95[ASN][1000 genomes]
rs732071	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs7320831	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7321120	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7321310	0.88[ASN][1000 genomes]
rs7321435	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs7327634	0.91[CHB][hapmap]
rs7332356	0.90[ASN][1000 genomes]
rs7338131	0.95[ASN][1000 genomes]
rs747781	0.91[CHB][hapmap]
rs755363	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7981050	0.87[MEX][hapmap]
rs7981904	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7991237	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7995946	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7998770	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9316563	0.87[CHB][hapmap]
rs9526819	0.87[CHB][hapmap]
rs9526823	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9526825	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9526826	0.95[ASN][1000 genomes]
rs9526834	0.96[ASN][1000 genomes]
rs9526835	0.94[ASN][1000 genomes]
rs9526836	1.00[ASN][1000 genomes]
rs9526837	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9526841	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526842	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9526843	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535812	0.91[CHB][hapmap]
rs9535822	0.86[CHB][hapmap]
rs9535825	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap]
rs9535826	0.87[CHB][hapmap]
rs9535832	0.91[CHB][hapmap]
rs9535836	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535845	0.95[ASN][1000 genomes]
rs9535851	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535853	0.90[ASN][1000 genomes]
rs9535856	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535858	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535861	0.91[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.84[ASN][1000 genomes]
rs9535862	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535866	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535867	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9535871	0.95[ASN][1000 genomes]
rs9535873	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs9535878	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535879	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9535880	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535882	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535883	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535885	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9535887	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535888	0.85[ASN][1000 genomes]
rs9535889	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9563089	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9568682	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs9568684	0.89[JPT][hapmap]
rs9568692	0.95[ASN][1000 genomes]
rs9568713	0.91[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	esv3429935	chr13:52694751-52735744	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7324458	NEK3	cis	Muscle Skeletal	GTEx
rs7324458	LECT1	cis	parietal	SCAN
rs7324458	CKAP2	cis	cerebellum	SCAN
rs7324458	CKAP2	cis	parietal	SCAN
rs7324458	ATP7B	cis	cerebellum	SCAN
rs7324458	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs7324458	NEK3	cis	Adipose Subcutaneous	GTEx
rs7324458	VPS36	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52703600-52709600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr13:52703600-52720400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr13:52703600-52725200	Weak transcription	Right Ventricle	heart
4	chr13:52703600-52725200	Weak transcription	Small Intestine	intestine
5	chr13:52703600-52725600	Weak transcription	Fetal Brain Male	brain
6	chr13:52703600-52730800	Weak transcription	Stomach Mucosa	stomach
7	chr13:52703600-52731000	Weak transcription	Brain Angular Gyrus	brain
8	chr13:52703600-52732600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr13:52703600-52732800	Weak transcription	Psoas Muscle	Psoas
10	chr13:52703600-52733000	Weak transcription	Esophagus	oesophagus
11	chr13:52703800-52709000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr13:52703800-52720000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr13:52703800-52720400	Weak transcription	HSMM	muscle
14	chr13:52703800-52723800	Weak transcription	Colonic Mucosa	Colon
15	chr13:52703800-52724800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr13:52703800-52731200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr13:52703800-52731400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr13:52703800-52731400	Weak transcription	Spleen	Spleen
19	chr13:52703800-52732600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr13:52703800-52732600	Weak transcription	HMEC	breast
21	chr13:52703800-52733200	Weak transcription	Gastric	stomach
22	chr13:52704000-52711000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr13:52704000-52733000	Weak transcription	Fetal Thymus	thymus
24	chr13:52704200-52708800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr13:52704200-52709600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr13:52704200-52709600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr13:52704200-52725400	Weak transcription	Primary T cells from cord blood	blood
28	chr13:52704800-52710400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr13:52704800-52727000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr13:52704800-52730000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr13:52705000-52710400	Strong transcription	Brain Germinal Matrix	brain
32	chr13:52705000-52711000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr13:52705000-52711200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr13:52705000-52712400	Strong transcription	HepG2	liver
35	chr13:52705000-52716200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr13:52705200-52709000	Strong transcription	Brain Substantia Nigra	brain
37	chr13:52705200-52709000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr13:52705200-52709200	Strong transcription	Left Ventricle	heart
39	chr13:52705200-52710400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr13:52705200-52710400	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr13:52705200-52710600	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr13:52705200-52710600	Strong transcription	Fetal Intestine Large	intestine
43	chr13:52705200-52710800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr13:52705200-52711000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr13:52705200-52712800	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr13:52705200-52713400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr13:52705200-52715800	Strong transcription	Adipose Nuclei	Adipose
48	chr13:52705200-52715800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr13:52705200-52719800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr13:52705400-52709200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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