Variant report

Variant	rs722579
Chromosome Location	chr16:70528224-70528225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:70527042..70530041-chr16:70532167..70534758,2	K562	blood:
2	chr16:70412713..70416394-chr16:70524042..70528993,5	MCF-7	breast:
3	chr16:70527930..70530251-chr16:70555794..70557376,2	K562	blood:
4	chr16:70520287..70522895-chr16:70527029..70528591,2	K562	blood:

Variant related genes	Relation type
ENSG00000260111	Chromatin interaction
ENSG00000103051	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 19 )

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

rs_ID	r²[population]
rs10852465	0.80[ASN][1000 genomes]
rs11075767	0.87[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11075768	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11075769	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11075770	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11640374	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs11641683	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11643344	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11643373	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs11643823	0.81[EUR][1000 genomes]
rs11645092	0.81[EUR][1000 genomes]
rs11645214	0.96[CEU][hapmap];0.84[GIH][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs11645287	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs11645437	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11645585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11648402	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11649624	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11865527	0.88[ASN][1000 genomes]
rs11866400	0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12447090	0.84[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs12597401	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12909	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12925729	0.87[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12933634	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2168606	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2288491	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2303791	0.88[MEX][hapmap];0.81[TSI][hapmap]
rs2303792	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2303793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33910368	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34567847	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34890962	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3762171	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3859068	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4277334	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4284632	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4324119	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4436771	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4513092	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4592653	0.96[CEU][hapmap];0.80[GIH][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs4985533	0.88[MEX][hapmap]
rs4985534	0.88[MEX][hapmap]
rs58963621	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6499320	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6499321	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71401814	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7189474	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs7190039	0.88[MEX][hapmap]
rs7192268	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs7194521	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7195030	0.81[ASN][1000 genomes]
rs7197262	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7197840	0.85[EUR][1000 genomes]
rs7198317	0.96[CEU][hapmap];0.84[GIH][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs7199859	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7200430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7201750	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7204583	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs744672	0.85[ASN][1000 genomes]
rs7919	0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs8045651	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046881	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8049641	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8049786	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8051506	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8052031	0.83[EUR][1000 genomes]
rs8052125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053436	0.81[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs8057610	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8058224	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs8062178	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8062183	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs8063990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8064013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936994	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs9635522	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9929904	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934440	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs9936225	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	esv2830027	chr16:70473934-70558039	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs722579	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs722579	RP11-296I10.6	cis	Artery Tibial	GTEx
rs722579	WWP2	cis	parietal	SCAN
rs722579	CLEC18A	cis	Artery Aorta	GTEx
rs722579	TMCO7	cis	parietal	SCAN
rs722579	EXOSC6	cis	parietal	SCAN
rs722579	LOC283970	cis	multi-tissue	Pritchard
rs722579	SF3B3	cis	parietal	SCAN
rs722579	PDPR	cis	cerebellum	SCAN
rs722579	RP11-296I10.6	cis	Nerve Tibial	GTEx
rs722579	SF3B3	cis	cerebellum	SCAN
rs722579	IL34	cis	parietal	SCAN
rs722579	PDPR	cis	parietal	SCAN
rs722579	WWP2	cis	cerebellum	SCAN
rs722579	CLEC18A	cis	Whole Blood	GTEx
rs722579	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs722579	EXOSC6	cis	cerebellum	SCAN
rs722579	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs722579	RP11-296I10.6	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70489400-70556400	Weak transcription	Stomach Mucosa	stomach
2	chr16:70501200-70535800	Strong transcription	Fetal Intestine Small	intestine
3	chr16:70501400-70535200	Strong transcription	Fetal Intestine Large	intestine
4	chr16:70501400-70536400	Strong transcription	Fetal Stomach	stomach
5	chr16:70504200-70532000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr16:70504400-70535200	Strong transcription	Liver	Liver
7	chr16:70506400-70535200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr16:70506600-70535400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr16:70511800-70535600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr16:70512000-70535400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr16:70512800-70533600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr16:70512800-70556400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr16:70513000-70528600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr16:70513800-70532200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr16:70516000-70530200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr16:70516800-70529400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr16:70516800-70529400	Weak transcription	HUVEC	blood vessel
18	chr16:70517600-70538800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr16:70518000-70545800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr16:70519000-70529400	Weak transcription	Fetal Kidney	kidney
21	chr16:70519800-70532200	Strong transcription	Primary T cells from cord blood	blood
22	chr16:70519800-70533400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr16:70522200-70532000	Strong transcription	Fetal Lung	lung
24	chr16:70522800-70531800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr16:70522800-70532200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr16:70523200-70535200	Strong transcription	Brain Germinal Matrix	brain
27	chr16:70523200-70542400	Weak transcription	Hela-S3	cervix
28	chr16:70523400-70535200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr16:70523400-70535200	Strong transcription	Dnd41	blood
30	chr16:70523600-70529200	Strong transcription	GM12878-XiMat	blood
31	chr16:70524000-70532200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr16:70524400-70529800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr16:70524400-70542400	Weak transcription	Fetal Brain Male	brain
34	chr16:70524600-70529400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr16:70524600-70529400	Weak transcription	NHDF-Ad	bronchial
36	chr16:70524600-70532000	Strong transcription	Lung	lung
37	chr16:70524600-70535200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr16:70525000-70528400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr16:70525200-70535200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr16:70525400-70535800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr16:70525600-70532000	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr16:70525600-70533400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr16:70525600-70534000	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr16:70525600-70535400	Strong transcription	Fetal Muscle Leg	muscle
45	chr16:70525600-70535800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr16:70525600-70538200	Strong transcription	Fetal Thymus	thymus
47	chr16:70525800-70533200	Strong transcription	Osteobl	bone
48	chr16:70525800-70533400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr16:70525800-70533800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr16:70525800-70535200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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