Variant report

Variant	rs17220369
Chromosome Location	chr22:31645421-31645422
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31642122..31645635-chr22:31666318..31668990,3	MCF-7	breast:
2	chr22:31642936..31645707-chr22:31684888..31688055,3	MCF-7	breast:
3	chr22:31607254..31610426-chr22:31643805..31645899,3	MCF-7	breast:
4	chr22:31643031..31646502-chr22:31653237..31655706,4	MCF-7	breast:
5	chr22:31642721..31645848-chr22:31739450..31742880,5	MCF-7	breast:
6	chr22:31642310..31646378-chr22:31653276..31655946,3	MCF-7	breast:
7	chr22:31555142..31556725-chr22:31643704..31646530,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100105	Chromatin interaction
ENSG00000264141	Chromatin interaction
ENSG00000182541	Chromatin interaction
ENSG00000213888	Chromatin interaction
ENSG00000100100	Chromatin interaction
ENSG00000138942	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1005624	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1034587	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10428007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11089491	0.89[ASN][1000 genomes]
rs12106582	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12627805	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12627941	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12628752	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2027982	0.91[JPT][hapmap]
rs2072193	0.81[JPT][hapmap]
rs2073858	0.89[ASN][1000 genomes]
rs2074735	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2239905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239906	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267169	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2267170	0.94[ASN][1000 genomes]
rs2267171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283878	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283880	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2413041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28514306	0.82[ASN][1000 genomes]
rs28709894	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34184692	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3761431	0.85[CHB][hapmap]
rs3788428	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4561750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4615	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4645077	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4820040	0.89[EUR][1000 genomes]
rs4820949	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4820952	0.88[ASN][1000 genomes]
rs4820964	0.88[ASN][1000 genomes]
rs4820965	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55737363	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55900008	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5749222	0.85[YRI][hapmap]
rs5749226	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5749231	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs5749232	0.82[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5749237	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749244	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749254	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs5753488	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753499	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753518	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs5753528	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753531	0.93[ASN][1000 genomes]
rs5753550	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5753551	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5753559	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs5753560	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753573	0.94[EUR][1000 genomes]
rs5753577	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58315696	0.84[ASN][1000 genomes]
rs5997898	0.91[JPT][hapmap]
rs5997940	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs61006749	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62236175	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62237396	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62237398	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62237399	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62237400	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62237404	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62237436	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68136222	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72617294	0.91[ASN][1000 genomes]
rs72617295	0.95[ASN][1000 genomes]
rs73158522	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs737809	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9609263	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459871	chr22:31551160-31680624	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	nsv588893	chr22:31551160-31680624	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31641200-31646600	Weak transcription	A549	lung
2	chr22:31641400-31649600	Weak transcription	Hela-S3	cervix
3	chr22:31642800-31648200	Enhancers	Stomach Mucosa	stomach
4	chr22:31643800-31645600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr22:31643800-31645600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr22:31643800-31646000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:31643800-31646600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr22:31644000-31645600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr22:31644000-31645800	Flanking Active TSS	NH-A	brain
10	chr22:31644000-31646400	Active TSS	Brain Hippocampus Middle	brain
11	chr22:31644000-31647200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
12	chr22:31644200-31645600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr22:31644200-31645800	Flanking Active TSS	Placenta	Placenta
14	chr22:31644200-31645800	Genic enhancers	Gastric	stomach
15	chr22:31644200-31646000	Active TSS	Fetal Kidney	kidney
16	chr22:31644200-31646000	Active TSS	Ovary	ovary
17	chr22:31644200-31646200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr22:31644200-31646200	Active TSS	HMEC	breast
19	chr22:31644200-31646200	Active TSS	HSMMtube	muscle
20	chr22:31644200-31646400	Active TSS	Esophagus	oesophagus
21	chr22:31644200-31649800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr22:31644200-31665800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr22:31644400-31645600	Weak transcription	HUVEC	blood vessel
24	chr22:31644600-31645600	Genic enhancers	Duodenum Mucosa	Duodenum
25	chr22:31644600-31645600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr22:31644600-31645800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
27	chr22:31644600-31645800	Genic enhancers	Primary T cells fromperipheralblood	blood
28	chr22:31644600-31645800	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr22:31644600-31645800	Flanking Active TSS	NHLF	lung
30	chr22:31644600-31646400	Weak transcription	Small Intestine	intestine
31	chr22:31644600-31647000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr22:31644600-31647600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr22:31644600-31647600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr22:31644600-31648200	Genic enhancers	Rectal Mucosa Donor 31	rectum
35	chr22:31644600-31649800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr22:31644600-31650400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr22:31644600-31654200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr22:31644600-31654200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr22:31644600-31654400	Weak transcription	K562	blood
40	chr22:31644600-31658000	Weak transcription	Psoas Muscle	Psoas
41	chr22:31644600-31668600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr22:31644800-31645600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr22:31644800-31645600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr22:31644800-31645600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr22:31644800-31645600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr22:31644800-31645600	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr22:31644800-31645800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr22:31644800-31645800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr22:31644800-31645800	Enhancers	Fetal Heart	heart
50	chr22:31644800-31646000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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