Variant report

Variant	rs5997917
Chromosome Location	chr22:31621792-31621793
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:31621716-31621840	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31619988..31622064-chr22:31622480..31625902,3	K562	blood:
2	chr22:31621605..31623830-chr22:31639235..31640827,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-1128P	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1034587	0.88[MEX][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap]
rs11089493	0.93[CEU][hapmap];0.81[TSI][hapmap]
rs11089495	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11089496	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1123705	0.87[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1138706	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11556237	0.93[CEU][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703005	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11703576	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11704156	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs11704523	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][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];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985726	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2057951	0.93[CEU][hapmap]
rs2899161	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs56292834	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5749231	0.88[MEX][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap]
rs57523999	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5753523	0.82[EUR][1000 genomes]
rs5997921	0.87[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs5997924	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997930	0.94[ASW][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs5997937	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs5997940	0.81[YRI][hapmap]
rs5997942	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]
rs5997948	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs5997959	0.93[CEU][hapmap]
rs713619	0.93[CEU][hapmap]
rs7285027	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7285716	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7286926	0.93[CEU][hapmap]
rs7287715	0.93[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs739428	0.93[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8143159	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8595	0.86[CEU][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3436353	chr22:31621628-31622558	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5997917	DUSP18	cis	cerebellum	SCAN
rs5997917	SFI1	cis	cerebellum	SCAN
rs5997917	DUSP18	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31608800-31639800	Weak transcription	Aorta	Aorta
2	chr22:31609200-31629000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr22:31609400-31621800	Weak transcription	Fetal Brain Female	brain
4	chr22:31609400-31625400	Weak transcription	NHLF	lung
5	chr22:31609400-31625400	Weak transcription	Osteobl	bone
6	chr22:31609600-31623000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr22:31609600-31623000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr22:31609600-31623400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr22:31609600-31624000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr22:31609600-31624800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr22:31609600-31625000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr22:31609600-31625400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr22:31609600-31625600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr22:31609600-31627200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr22:31609600-31639200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr22:31609800-31621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr22:31609800-31629400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr22:31612400-31622800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr22:31612600-31621800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr22:31613800-31622800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr22:31614000-31626600	Weak transcription	Fetal Heart	heart
22	chr22:31614400-31625200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr22:31614800-31625200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr22:31615000-31625000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr22:31615000-31625000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr22:31615000-31626400	Weak transcription	Fetal Kidney	kidney
27	chr22:31615200-31623000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr22:31615200-31625200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr22:31615200-31625200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr22:31615200-31625200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr22:31615200-31625200	Weak transcription	Left Ventricle	heart
32	chr22:31615200-31625200	Weak transcription	NHDF-Ad	bronchial
33	chr22:31615200-31625400	Weak transcription	Esophagus	oesophagus
34	chr22:31615200-31626200	Weak transcription	HSMMtube	muscle
35	chr22:31615200-31629000	Weak transcription	NH-A	brain
36	chr22:31615600-31625400	Weak transcription	NHEK	skin
37	chr22:31616200-31625000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr22:31616200-31625400	Weak transcription	HMEC	breast
39	chr22:31616600-31623200	Weak transcription	A549	lung
40	chr22:31616600-31625400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr22:31616800-31623200	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr22:31617400-31621800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr22:31617800-31625200	Weak transcription	Brain Germinal Matrix	brain
44	chr22:31618200-31625400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr22:31618200-31625800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr22:31619200-31621800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr22:31619200-31622000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr22:31619200-31622000	Weak transcription	Placenta	Placenta
49	chr22:31619200-31625600	Weak transcription	Ovary	ovary
50	chr22:31619400-31621800	Weak transcription	Fetal Thymus	thymus

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