Variant report

Variant	rs1041875
Chromosome Location	chr22:33710214-33710215
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1008212	0.92[EUR][1000 genomes]
rs12484156	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12484639	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1807662	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1967965	1.00[CEU][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs2157197	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2187745	0.83[CEU][hapmap]
rs2267189	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2267190	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2267191	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2283886	0.91[EUR][1000 genomes]
rs2283887	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2285105	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35340305	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3884933	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs739022	0.96[CEU][hapmap];0.93[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8137330	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8138543	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8142819	0.84[EUR][1000 genomes]
rs9607031	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9609758	0.85[EUR][1000 genomes]
rs9609759	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531587	chr22:33346710-33809338	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1067068	chr22:33452180-33851033	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
4	nsv933455	chr22:33532697-33915429	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1064192	chr22:33615699-33741836	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1059927	chr22:33615699-33904339	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv544682	chr22:33615699-33904339	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1060316	chr22:33644676-33737725	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1056097	chr22:33650328-33733456	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1061485	chr22:33670971-33885169	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1055475	chr22:33680854-33710571	Genic enhancers Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1060896	chr22:33698546-33729763	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1059522	chr22:33706201-33728482	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1041875	INPP5J	cis	parietal	SCAN
rs1041875	TTC28AS	cis	parietal	SCAN
rs1041875	PES1	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33660000-33722800	Weak transcription	HSMMtube	muscle
2	chr22:33666800-33713600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr22:33667600-33724800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr22:33668400-33712200	Weak transcription	Esophagus	oesophagus
5	chr22:33668800-33720400	Weak transcription	Psoas Muscle	Psoas
6	chr22:33672600-33711800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr22:33673400-33726400	Weak transcription	Colonic Mucosa	Colon
8	chr22:33673400-33735000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr22:33676600-33745000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr22:33679400-33713800	Weak transcription	Brain Germinal Matrix	brain
11	chr22:33679400-33733200	Weak transcription	Fetal Brain Female	brain
12	chr22:33679400-33743800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr22:33690200-33718400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:33692600-33711200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr22:33693000-33710400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr22:33696200-33725000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr22:33696200-33748000	Weak transcription	Fetal Lung	lung
18	chr22:33696400-33725000	Weak transcription	Stomach Mucosa	stomach
19	chr22:33696600-33721600	Weak transcription	Fetal Kidney	kidney
20	chr22:33698400-33718400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr22:33698600-33736400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr22:33698800-33719800	Weak transcription	HepG2	liver
23	chr22:33699000-33710400	Weak transcription	Colon Smooth Muscle	Colon
24	chr22:33699000-33711400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr22:33699200-33713800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr22:33699400-33714400	Weak transcription	Brain Substantia Nigra	brain
27	chr22:33699400-33722800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr22:33699400-33731800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr22:33700000-33713200	Weak transcription	GM12878-XiMat	blood
30	chr22:33700600-33714800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr22:33700600-33715200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr22:33704200-33715800	Weak transcription	Fetal Brain Male	brain
33	chr22:33704400-33712400	Strong transcription	Fetal Stomach	stomach
34	chr22:33704600-33723400	Weak transcription	Aorta	Aorta
35	chr22:33706000-33712600	Strong transcription	Left Ventricle	heart
36	chr22:33706000-33712800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr22:33707000-33720400	Weak transcription	Fetal Heart	heart
38	chr22:33707400-33712400	Strong transcription	Stomach Smooth Muscle	stomach
39	chr22:33708000-33712200	Strong transcription	Fetal Intestine Large	intestine
40	chr22:33708400-33711600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr22:33708400-33712600	Strong transcription	Fetal Intestine Small	intestine
42	chr22:33708600-33712000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr22:33708600-33712200	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr22:33708600-33712400	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr22:33708800-33711400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr22:33708800-33712400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr22:33709000-33710800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr22:33709000-33710800	Strong transcription	Gastric	stomach
49	chr22:33709000-33712200	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr22:33709000-33712400	Strong transcription	Ovary	ovary

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