Variant report

Variant	rs9925780
Chromosome Location	chr16:81045176-81045177
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81043779..81046119-chr16:81060874..81062593,2	MCF-7	breast:
2	chr16:81042328..81045873-chr16:81053654..81056834,3	MCF-7	breast:
3	chr16:81030715..81033502-chr16:81044957..81046578,2	K562	blood:

Variant related genes	Relation type
ENSG00000103121	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs11150333	0.85[AMR][1000 genomes]
rs11150334	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11150335	0.96[ASN][1000 genomes]
rs1127390	0.89[EUR][1000 genomes]
rs11864367	0.81[EUR][1000 genomes]
rs11866803	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12446304	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12446810	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12448656	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12928638	0.83[GIH][hapmap]
rs13331118	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13332890	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13332902	0.83[EUR][1000 genomes]
rs13334887	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13336292	0.83[EUR][1000 genomes]
rs13336629	0.83[EUR][1000 genomes]
rs1453327	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1453328	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1469123	0.94[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1469124	0.94[CEU][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1469125	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1469126	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1477381	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs1549288	0.96[MEX][hapmap]
rs16954366	0.91[TSI][hapmap]
rs16954399	0.80[GIH][hapmap]
rs1964298	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2018122	0.81[EUR][1000 genomes]
rs2098726	0.90[EUR][1000 genomes]
rs2113196	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2113197	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2167889	0.90[EUR][1000 genomes]
rs2216753	0.90[GIH][hapmap];0.92[MEX][hapmap]
rs2244452	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2287991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2316923	0.91[EUR][1000 genomes]
rs2549822	0.86[TSI][hapmap]
rs2549828	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs2549833	0.90[EUR][1000 genomes]
rs2549834	0.86[TSI][hapmap]
rs2549835	0.89[EUR][1000 genomes]
rs2549836	0.90[EUR][1000 genomes]
rs2549837	0.90[EUR][1000 genomes]
rs2549838	0.90[EUR][1000 genomes]
rs2549839	0.90[EUR][1000 genomes]
rs2549840	0.90[EUR][1000 genomes]
rs2549841	0.94[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2549842	0.94[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs2549843	0.90[EUR][1000 genomes]
rs2549844	0.87[EUR][1000 genomes]
rs2549846	0.90[EUR][1000 genomes]
rs2549847	0.90[EUR][1000 genomes]
rs2549848	0.90[EUR][1000 genomes]
rs2549852	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2549853	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2549854	0.94[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2549855	0.94[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2549856	0.94[CEU][hapmap];0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2549857	0.94[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2549858	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2549859	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2549860	0.86[TSI][hapmap]
rs2549861	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2549863	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2549879	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2549883	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2549886	0.90[EUR][1000 genomes]
rs2549887	0.94[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs2549888	0.88[EUR][1000 genomes]
rs2602411	0.90[GIH][hapmap];0.92[MEX][hapmap]
rs2602413	0.93[GIH][hapmap];0.92[MEX][hapmap]
rs2602423	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2602424	1.00[CEU][hapmap];0.96[GIH][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2602426	0.88[EUR][1000 genomes]
rs2602433	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2602434	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2602443	0.93[GIH][hapmap];0.92[MEX][hapmap]
rs2602446	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2602448	0.90[EUR][1000 genomes]
rs2602449	0.90[EUR][1000 genomes]
rs2602453	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2911148	0.90[EUR][1000 genomes]
rs2911150	0.94[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2970079	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2970080	0.86[TSI][hapmap]
rs2970083	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2970084	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2970085	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2970086	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3743503	0.83[GIH][hapmap]
rs3784814	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3826048	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55776427	0.84[EUR][1000 genomes]
rs56306230	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62054241	0.81[EUR][1000 genomes]
rs6564814	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66516157	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71400133	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7196960	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7197370	1.00[CEU][hapmap]
rs8049565	0.80[GIH][hapmap]
rs874053	0.88[EUR][1000 genomes]
rs874054	0.88[EUR][1000 genomes]
rs9888895	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9889194	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9921448	0.88[EUR][1000 genomes]
rs9921914	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9923948	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9931292	0.88[EUR][1000 genomes]
rs9932857	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9934957	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9936366	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9937731	0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9938541	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9939934	0.86[TSI][hapmap]

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	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1065258	chr16:80887483-81081768	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1058045	chr16:80918138-81048242	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS 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 miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9925780	CENPN	cis	lymphoblastoid	seeQTL
rs9925780	HSD17B2	cis	cerebellum	SCAN
rs9925780	CENPN	cis	parietal	SCAN
rs9925780	CENPN	Cis_1M	lymphoblastoid	RTeQTL
rs9925780	C16orf61	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81041600-81047600	Weak transcription	Spleen	Spleen
2	chr16:81041800-81053600	Weak transcription	Gastric	stomach
3	chr16:81041800-81069000	Weak transcription	Ovary	ovary
4	chr16:81041800-81069000	Weak transcription	Small Intestine	intestine
5	chr16:81042000-81045600	Weak transcription	Liver	Liver
6	chr16:81042000-81046200	Weak transcription	Brain Substantia Nigra	brain
7	chr16:81042000-81046200	Weak transcription	Right Atrium	heart
8	chr16:81042000-81047000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr16:81042000-81047400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr16:81042000-81047800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr16:81042000-81047800	Weak transcription	Aorta	Aorta
12	chr16:81042000-81047800	Weak transcription	Right Ventricle	heart
13	chr16:81042000-81048000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr16:81042000-81048200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr16:81042000-81048200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr16:81042000-81053000	Weak transcription	Brain Angular Gyrus	brain
17	chr16:81042000-81053600	Weak transcription	HSMMtube	muscle
18	chr16:81042000-81054400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr16:81042000-81054800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr16:81042000-81057600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr16:81042000-81058400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr16:81042000-81069000	Weak transcription	Esophagus	oesophagus
23	chr16:81042000-81069000	Weak transcription	Pancreas	Pancrea
24	chr16:81042000-81069600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr16:81042200-81045400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr16:81042200-81045400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr16:81042200-81045600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr16:81042200-81046200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr16:81042200-81046600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr16:81042200-81046600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr16:81042200-81046600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr16:81042200-81046600	Weak transcription	Fetal Kidney	kidney
33	chr16:81042200-81046600	Weak transcription	NH-A	brain
34	chr16:81042200-81046800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr16:81042200-81046800	Weak transcription	Primary T cells from cord blood	blood
36	chr16:81042200-81046800	Weak transcription	Adipose Nuclei	Adipose
37	chr16:81042200-81046800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr16:81042200-81046800	Weak transcription	Fetal Intestine Small	intestine
39	chr16:81042200-81046800	Weak transcription	Fetal Stomach	stomach
40	chr16:81042200-81046800	Weak transcription	Left Ventricle	heart
41	chr16:81042200-81047000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr16:81042200-81047000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr16:81042200-81047000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr16:81042200-81047000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr16:81042200-81047400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr16:81042200-81047600	Weak transcription	Fetal Brain Female	brain
47	chr16:81042200-81047800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr16:81042200-81047800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr16:81042200-81047800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr16:81042200-81048200	Weak transcription	Brain Anterior Caudate	brain

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