Variant report

Variant	rs9898265
Chromosome Location	chr17:20940688-20940689
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20932232..20934940-chr17:20938795..20941578,2	MCF-7	breast:
2	chr17:20934273..20942906-chr17:20943761..20949798,22	MCF-7	breast:
3	chr17:20936833..20939628-chr17:20939684..20941380,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124422	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1038107	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1038109	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1044410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1044414	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1044420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204326	0.91[ASW][hapmap];0.86[YRI][hapmap]
rs11204330	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1127815	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12103803	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12150138	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12600604	0.82[EUR][1000 genomes]
rs1904230	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1993901	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];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2009756	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2127094	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2291036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2291037	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364327	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2364328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2364329	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364330	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364331	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2364333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816664	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3943299	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4462662	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4613123	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985813	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985820	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985824	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4985935	0.91[JPT][hapmap]
rs4985941	0.95[CEU][hapmap];0.91[JPT][hapmap]
rs4985948	0.95[CEU][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4985949	0.87[AMR][1000 genomes]
rs4985952	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4985953	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4985954	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4985955	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4985957	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4985962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4985964	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4985974	0.95[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes]
rs5005801	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6587115	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71371043	0.89[ASN][1000 genomes]
rs7207724	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7207753	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7208779	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7211094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7213684	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7215369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7216090	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7216145	0.85[YRI][hapmap]
rs7216449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7216786	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7216978	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7218112	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs7218443	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7219244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7221483	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7221757	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7223388	0.95[CEU][hapmap];0.91[JPT][hapmap]
rs7224746	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7226229	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8064435	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8071311	0.80[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs8075790	0.86[JPT][hapmap]
rs8076078	0.82[EUR][1000 genomes]
rs8077998	0.85[ASN][1000 genomes]
rs880652	0.86[JPT][hapmap]
rs899335	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs899336	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs899338	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs899341	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs899342	0.95[CEU][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs961004	0.82[EUR][1000 genomes]
rs9797279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9894624	0.87[ASN][1000 genomes]
rs9895047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9896259	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9896301	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9902303	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs996065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv827917	chr17:20896100-20961777	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9898265	SLC5A10	cis	parietal	SCAN
rs9898265	FAM27L	cis	cerebellum	SCAN
rs9898265	USP22	cis	Whole Blood	GTEx
rs9898265	USP22	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20923000-20943800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:20932200-20941400	Genic enhancers	A549	lung
3	chr17:20932800-20941800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:20934000-20942800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr17:20934000-20943200	Weak transcription	Esophagus	oesophagus
6	chr17:20935000-20941000	Enhancers	Right Ventricle	heart
7	chr17:20935200-20943800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr17:20935600-20942200	Enhancers	Fetal Brain Male	brain
9	chr17:20936200-20941600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr17:20936400-20940800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr17:20936600-20941000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr17:20936600-20941200	Genic enhancers	HUVEC	blood vessel
13	chr17:20936800-20941800	Genic enhancers	NHEK	skin
14	chr17:20936800-20942000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr17:20936800-20943800	Enhancers	Liver	Liver
16	chr17:20937400-20941200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr17:20937400-20941200	Enhancers	Colonic Mucosa	Colon
18	chr17:20937600-20941400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr17:20937600-20942000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
20	chr17:20938000-20941600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:20938000-20941800	Enhancers	Colon Smooth Muscle	Colon
22	chr17:20938200-20941200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr17:20938200-20943600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr17:20938400-20940800	Enhancers	Brain Hippocampus Middle	brain
25	chr17:20938400-20940800	Enhancers	HSMMtube	muscle
26	chr17:20938400-20941200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr17:20938400-20941400	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr17:20938400-20941400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr17:20938400-20941800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr17:20938400-20943200	Weak transcription	Lung	lung
31	chr17:20938400-20944000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr17:20938800-20941400	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr17:20938800-20941400	Enhancers	NH-A	brain
34	chr17:20938800-20941800	Genic enhancers	Rectal Mucosa Donor 29	rectum
35	chr17:20939000-20943200	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr17:20939200-20942200	Genic enhancers	Primary hematopoietic stem cells	blood
37	chr17:20939200-20942800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr17:20939400-20940800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr17:20939400-20940800	Genic enhancers	Thymus	Thymus
40	chr17:20939400-20941000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr17:20939400-20941000	Enhancers	Gastric	stomach
42	chr17:20939400-20941000	Transcr. at gene 5' and 3'	Dnd41	blood
43	chr17:20939400-20941200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr17:20939400-20941200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
45	chr17:20939400-20941200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr17:20939400-20941200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr17:20939400-20941400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
48	chr17:20939400-20941400	Genic enhancers	Fetal Lung	lung
49	chr17:20939400-20941800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr17:20939400-20941800	Enhancers	Small Intestine	intestine

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