Variant report

Variant	rs11089495
Chromosome Location	chr22:31685129-31685130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr22:31685106-31685196	HepG2	liver:	n/a	chr22:31685148-31685166
2	MAFK	chr22:31685121-31685171	HepG2	liver:	n/a	chr22:31685149-31685164
3	SPI1	chr22:31684856-31685345	HL-60	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:31675823..31681003-chr22:31682955..31686672,6	MCF-7	breast:
2	chr22:31659364..31661721-chr22:31683872..31686646,3	MCF-7	breast:
3	chr22:31683915..31694680-chr22:31733392..31744713,34	MCF-7	breast:
4	chr22:31679718..31681431-chr22:31684803..31686641,2	K562	blood:
5	chr22:31683610..31686152-chr22:31686912..31689729,2	MCF-7	breast:
6	chr22:31667817..31670473-chr22:31682402..31685348,3	K562	blood:
7	chr22:31684664..31691252-chr22:31735490..31744100,29	MCF-7	breast:
8	chr22:31642936..31645707-chr22:31684888..31688055,3	MCF-7	breast:
9	chr22:31684558..31686657-chr22:31740463..31743342,2	K562	blood:
10	chr10:101184624..101186124-chr22:31683739..31685259,2	K562	blood:
11	chr22:31682441..31684194-chr22:31684357..31686395,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228839	TF binding region
ENSG00000100105	Chromatin interaction
ENSG00000228839	Chromatin interaction
ENSG00000213888	Chromatin interaction
ENSG00000182541	Chromatin interaction
ENSG00000100100	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];0.85[MKK][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes]
rs11089493	1.00[CEU][hapmap];0.84[GIH][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs11089496	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1123705	0.94[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1138706	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11556237	0.87[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11703005	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11703576	0.97[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];0.87[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12157877	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs16989459	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs16989469	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1985726	0.82[AMR][1000 genomes]
rs2057951	1.00[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs2899161	0.94[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs3091392	0.87[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap]
rs4293639	0.94[EUR][1000 genomes]
rs4820972	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs55837074	0.80[EUR][1000 genomes]
rs56292834	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5749231	0.84[ASW][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap]
rs57523999	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5753523	0.96[EUR][1000 genomes]
rs5753554	0.91[EUR][1000 genomes]
rs5753629	0.89[ASN][1000 genomes]
rs5994386	0.94[EUR][1000 genomes]
rs5994387	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997917	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]
rs5997921	0.94[CEU][hapmap];0.80[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs5997924	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5997930	0.89[ASW][hapmap];0.92[LWK][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs5997937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5997940	0.81[YRI][hapmap]
rs5997942	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]
rs5997948	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997956	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997959	1.00[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs5997965	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60459126	0.84[EUR][1000 genomes]
rs695455	0.87[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap]
rs695682	0.87[CEU][hapmap]
rs713619	1.00[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs7285027	0.95[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];0.89[EUR][1000 genomes]
rs7286926	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7287715	0.87[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs738658	0.82[GIH][hapmap];0.94[MEX][hapmap]
rs739428	0.87[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8143159	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8595	0.93[CEU][hapmap]
rs9680708	0.92[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
rs11089495	SFI1	cis	cerebellum	SCAN
rs11089495	DUSP18	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	chr22:31669000-31685600	Weak transcription	Fetal Brain Male	brain
4	chr22:31669000-31686000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr22:31671800-31686200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr22:31672600-31685600	Strong transcription	Brain Germinal Matrix	brain
7	chr22:31673800-31685600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr22:31674200-31685400	Strong transcription	Fetal Brain Female	brain
9	chr22:31674400-31686400	Weak transcription	Fetal Kidney	kidney
10	chr22:31674400-31686400	Weak transcription	NHDF-Ad	bronchial
11	chr22:31675400-31686400	Weak transcription	NH-A	brain
12	chr22:31678000-31686400	Weak transcription	HMEC	breast
13	chr22:31679000-31685400	Weak transcription	Liver	Liver
14	chr22:31679200-31685800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr22:31679200-31686400	Weak transcription	HSMM	muscle
16	chr22:31679200-31686600	Weak transcription	Ovary	ovary
17	chr22:31679400-31685200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr22:31679400-31685800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr22:31679400-31686400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr22:31680000-31685200	Genic enhancers	Fetal Thymus	thymus
21	chr22:31680000-31685200	Weak transcription	NHEK	skin
22	chr22:31680200-31685400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr22:31680400-31685200	Genic enhancers	Brain Anterior Caudate	brain
24	chr22:31680400-31685200	Genic enhancers	Brain Cingulate Gyrus	brain
25	chr22:31680400-31685200	Genic enhancers	Brain Substantia Nigra	brain
26	chr22:31680400-31685400	Genic enhancers	Brain Inferior Temporal Lobe	brain
27	chr22:31680400-31688400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
28	chr22:31680600-31685200	Weak transcription	Esophagus	oesophagus
29	chr22:31680600-31685600	Genic enhancers	Primary B cells from peripheral blood	blood
30	chr22:31680600-31685800	Genic enhancers	Brain Angular Gyrus	brain
31	chr22:31680600-31687200	Transcr. at gene 5' and 3'	Thymus	Thymus
32	chr22:31680800-31685600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr22:31680800-31685800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr22:31681000-31686600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
35	chr22:31681200-31685200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr22:31681200-31685200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr22:31681200-31685200	Genic enhancers	Adipose Nuclei	Adipose
38	chr22:31681200-31685600	Weak transcription	Fetal Muscle Leg	muscle
39	chr22:31681200-31686000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr22:31681200-31686200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr22:31681200-31686400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr22:31681200-31686400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr22:31681400-31685200	Weak transcription	K562	blood
44	chr22:31682200-31685600	Genic enhancers	Primary monocytes fromperipheralblood	blood
45	chr22:31682200-31685600	Strong transcription	HSMMtube	muscle
46	chr22:31682600-31685400	Genic enhancers	Stomach Smooth Muscle	stomach
47	chr22:31682600-31685600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr22:31682600-31685600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
49	chr22:31682600-31687400	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
50	chr22:31682800-31685200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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