Variant report

Variant	rs11556237
Chromosome Location	chr22:31644614-31644615
allele	C/T
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
ENSG00000100100	Chromatin interaction
ENSG00000182541	Chromatin interaction
ENSG00000213888	Chromatin interaction
ENSG00000138942	Chromatin interaction
ENSG00000264141	Chromatin interaction
ENSG00000100105	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1034587	0.82[MEX][hapmap]
rs11089493	0.87[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs11089495	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]
rs11089496	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1123705	0.81[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1138706	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703005	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11703576	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11704156	0.86[MEX][hapmap]
rs11704523	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12157877	0.86[CEU][hapmap]
rs16989459	0.86[MEX][hapmap]
rs16989469	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985726	0.83[AMR][1000 genomes]
rs2057951	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs2899161	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs3091392	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs4293639	0.81[EUR][1000 genomes]
rs4820972	0.86[MEX][hapmap]
rs55837074	0.87[EUR][1000 genomes]
rs56292834	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5749231	0.82[MEX][hapmap]
rs57523999	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5753523	0.87[EUR][1000 genomes]
rs59473370	0.80[AMR][1000 genomes]
rs5994386	0.81[EUR][1000 genomes]
rs5994387	0.80[EUR][1000 genomes]
rs5997917	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]
rs5997921	0.81[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs5997924	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997937	0.87[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs5997942	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]
rs5997948	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5997956	0.80[EUR][1000 genomes]
rs5997959	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs5997965	0.80[EUR][1000 genomes]
rs695455	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs695682	1.00[CEU][hapmap]
rs713619	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs7285027	0.85[EUR][1000 genomes]
rs7285716	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7286926	0.87[CEU][hapmap]
rs7287715	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs7291131	0.80[AFR][1000 genomes]
rs738658	0.92[GIH][hapmap];0.87[MEX][hapmap]
rs739428	0.87[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8143159	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8595	1.00[ASN][1000 genomes]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11556237	DUSP18	cis	cerebellum	SCAN
rs11556237	DUSP18	cis	parietal	SCAN
rs11556237	SFI1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31641200-31645000	Weak transcription	GM12878-XiMat	blood
2	chr22:31641200-31646600	Weak transcription	A549	lung
3	chr22:31641400-31649600	Weak transcription	Hela-S3	cervix
4	chr22:31642800-31644800	Strong transcription	HepG2	liver
5	chr22:31642800-31648200	Enhancers	Stomach Mucosa	stomach
6	chr22:31643000-31644800	Enhancers	Primary hematopoietic stem cells	blood
7	chr22:31643000-31644800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr22:31643000-31645000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr22:31643400-31644800	Enhancers	Primary B cells from cord blood	blood
10	chr22:31643400-31645200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr22:31643600-31644800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr22:31643600-31644800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr22:31643800-31644800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr22:31643800-31644800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr22:31643800-31644800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr22:31643800-31644800	Flanking Active TSS	Colonic Mucosa	Colon
17	chr22:31643800-31644800	Flanking Active TSS	Fetal Heart	heart
18	chr22:31643800-31644800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr22:31643800-31645000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:31643800-31645000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr22:31643800-31645000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr22:31643800-31645000	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr22:31643800-31645200	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr22:31643800-31645200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
25	chr22:31643800-31645400	Flanking Active TSS	Fetal Muscle Trunk	muscle
26	chr22:31643800-31645400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr22:31643800-31645400	Genic enhancers	Spleen	Spleen
28	chr22:31643800-31645600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr22:31643800-31645600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr22:31643800-31646000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr22:31643800-31646600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr22:31644000-31644800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr22:31644000-31644800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr22:31644000-31644800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr22:31644000-31644800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr22:31644000-31644800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr22:31644000-31644800	Active TSS	Colon Smooth Muscle	Colon
38	chr22:31644000-31644800	Active TSS	Fetal Brain Female	brain
39	chr22:31644000-31644800	Flanking Active TSS	Fetal Lung	lung
40	chr22:31644000-31644800	Flanking Active TSS	Fetal Thymus	thymus
41	chr22:31644000-31645000	Active TSS	Brain Anterior Caudate	brain
42	chr22:31644000-31645000	Active TSS	Brain Germinal Matrix	brain
43	chr22:31644000-31645000	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
44	chr22:31644000-31645200	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr22:31644000-31645200	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr22:31644000-31645200	Active TSS	Brain Cingulate Gyrus	brain
47	chr22:31644000-31645200	Active TSS	Right Atrium	heart
48	chr22:31644000-31645400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr22:31644000-31645400	Active TSS	Brain Angular Gyrus	brain
50	chr22:31644000-31645400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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