Variant report

Variant	rs5997942
Chromosome Location	chr22:31682448-31682449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31681629..31683891-chr22:31739597..31743565,3	MCF-7	breast:
2	chr22:31680141..31683839-chr22:31741911..31744786,3	MCF-7	breast:
3	chr22:31667817..31670473-chr22:31682402..31685348,3	K562	blood:
4	chr22:31682441..31684194-chr22:31684357..31686395,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100105	Chromatin interaction
ENSG00000213888	Chromatin interaction
ENSG00000182541	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1034587	0.84[ASW][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes]
rs11089493	0.93[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs11089495	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11089496	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1123705	0.87[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1138706	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11556237	0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11703005	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11703576	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11704156	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs11704523	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12157877	0.93[CEU][hapmap];0.96[YRI][hapmap]
rs16989459	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs16989469	0.93[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1985726	0.82[AMR][1000 genomes]
rs2057951	0.93[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs2899161	0.87[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs3091392	0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs4293639	0.89[EUR][1000 genomes]
rs4820972	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs55837074	0.81[EUR][1000 genomes]
rs56292834	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5749231	0.84[ASW][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap]
rs57523999	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5753523	0.95[EUR][1000 genomes]
rs5753554	0.86[EUR][1000 genomes]
rs5753629	0.89[ASN][1000 genomes]
rs5994386	0.89[EUR][1000 genomes]
rs5994387	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997917	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5997921	0.87[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs5997924	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5997930	0.89[ASW][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs5997937	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs5997940	0.81[YRI][hapmap]
rs5997948	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997956	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997959	0.93[CEU][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs5997965	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60459126	0.85[EUR][1000 genomes]
rs695455	0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs695682	0.93[CEU][hapmap]
rs713619	0.93[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs7285027	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7285716	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7286926	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs7287715	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs738658	0.82[CEU][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap]
rs739428	0.93[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8143159	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8595	0.86[CEU][hapmap]
rs9680708	0.87[EUR][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	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
2	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
3	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5997942	DUSP18	cis	cerebellum	SCAN
rs5997942	SFI1	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31654000-31685600	Strong transcription	Fetal Stomach	stomach
2	chr22:31659000-31685600	Weak transcription	Psoas Muscle	Psoas
3	chr22:31666000-31682600	Strong transcription	Skeletal Muscle Female	skeletal muscle
4	chr22:31666000-31684200	Strong transcription	Aorta	Aorta
5	chr22:31667000-31684600	Weak transcription	Right Atrium	heart
6	chr22:31669000-31685600	Weak transcription	Fetal Brain Male	brain
7	chr22:31669000-31686000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr22:31669200-31682600	Strong transcription	Stomach Smooth Muscle	stomach
9	chr22:31671200-31684600	Weak transcription	Fetal Heart	heart
10	chr22:31671800-31686200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr22:31672600-31685600	Strong transcription	Brain Germinal Matrix	brain
12	chr22:31673800-31685600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr22:31674000-31683800	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr22:31674200-31682600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr22:31674200-31685400	Strong transcription	Fetal Brain Female	brain
16	chr22:31674400-31686400	Weak transcription	Fetal Kidney	kidney
17	chr22:31674400-31686400	Weak transcription	NHDF-Ad	bronchial
18	chr22:31674600-31682600	Strong transcription	Rectal Smooth Muscle	rectum
19	chr22:31675400-31686400	Weak transcription	NH-A	brain
20	chr22:31675800-31685000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr22:31676400-31684600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr22:31676800-31684800	Weak transcription	Hela-S3	cervix
23	chr22:31676800-31685000	Weak transcription	Osteobl	bone
24	chr22:31677000-31684600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr22:31678000-31686400	Weak transcription	HMEC	breast
26	chr22:31678200-31684000	Strong transcription	Left Ventricle	heart
27	chr22:31678800-31682600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr22:31679000-31685400	Weak transcription	Liver	Liver
29	chr22:31679200-31685000	Weak transcription	Fetal Lung	lung
30	chr22:31679200-31685800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr22:31679200-31686400	Weak transcription	HSMM	muscle
32	chr22:31679200-31686600	Weak transcription	Ovary	ovary
33	chr22:31679400-31684800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr22:31679400-31685200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr22:31679400-31685800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr22:31679400-31686400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr22:31679600-31684000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr22:31680000-31685200	Genic enhancers	Fetal Thymus	thymus
39	chr22:31680000-31685200	Weak transcription	NHEK	skin
40	chr22:31680200-31684400	Enhancers	Primary hematopoietic stem cells	blood
41	chr22:31680200-31685400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr22:31680400-31682800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr22:31680400-31682800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
44	chr22:31680400-31683000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr22:31680400-31683000	Genic enhancers	Brain Hippocampus Middle	brain
46	chr22:31680400-31683000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr22:31680400-31683000	Genic enhancers	Lung	lung
48	chr22:31680400-31683000	Enhancers	HUVEC	blood vessel
49	chr22:31680400-31683200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
50	chr22:31680400-31684000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood

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