Variant report

Variant	rs134187
Chromosome Location	chr22:28641134-28641135
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs134170	0.96[LWK][hapmap];0.84[AFR][1000 genomes]
rs134174	0.86[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs134184	0.88[AFR][1000 genomes]
rs134185	0.84[ASW][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes]
rs135640	0.86[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[LWK][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs16986354	0.85[LWK][hapmap]
rs5762481	0.84[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap]
rs5762549	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs5762552	0.95[CHB][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9608667	0.81[LWK][hapmap]

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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs134187	TTC28AS	cis	cerebellum	SCAN
rs134187	CRYBB2P1	cis	parietal	SCAN
rs134187	SUSD2	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28618400-28662200	Weak transcription	Pancreas	Pancrea
2	chr22:28628200-28643200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr22:28635600-28650800	Weak transcription	Dnd41	blood
4	chr22:28638400-28642000	Enhancers	K562	blood
5	chr22:28639400-28641200	Enhancers	Fetal Brain Male	brain
6	chr22:28639400-28642200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr22:28639400-28643200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr22:28639400-28643600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr22:28639400-28643800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr22:28639400-28644000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr22:28639400-28644200	Enhancers	Osteobl	bone
12	chr22:28639400-28645800	Enhancers	Fetal Heart	heart
13	chr22:28639600-28641200	Enhancers	Psoas Muscle	Psoas
14	chr22:28639600-28641800	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr22:28639600-28641800	Enhancers	NHDF-Ad	bronchial
16	chr22:28639600-28642200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr22:28639600-28642800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr22:28639600-28643200	Enhancers	HSMM	muscle
19	chr22:28639600-28644000	Enhancers	NH-A	brain
20	chr22:28639800-28641800	Weak transcription	Adipose Nuclei	Adipose
21	chr22:28639800-28643000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr22:28639800-28643000	Weak transcription	Gastric	stomach
23	chr22:28639800-28643000	Weak transcription	Left Ventricle	heart
24	chr22:28639800-28643200	Weak transcription	Right Ventricle	heart
25	chr22:28640200-28642000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr22:28640200-28642000	Enhancers	Brain Substantia Nigra	brain
27	chr22:28640200-28642200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr22:28640400-28641200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr22:28640400-28641600	Enhancers	Fetal Lung	lung
30	chr22:28640600-28641800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr22:28640600-28642400	Enhancers	Fetal Intestine Large	intestine
32	chr22:28640800-28641400	Enhancers	Brain Hippocampus Middle	brain
33	chr22:28640800-28641600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr22:28640800-28641800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr22:28640800-28641800	Enhancers	Fetal Intestine Small	intestine
36	chr22:28640800-28641800	Enhancers	Stomach Mucosa	stomach
37	chr22:28640800-28642000	Enhancers	Liver	Liver
38	chr22:28640800-28642000	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr22:28640800-28642000	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr22:28640800-28642600	Enhancers	A549	lung
41	chr22:28640800-28643400	Enhancers	HSMMtube	muscle
42	chr22:28640800-28644000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
43	chr22:28640800-28644200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr22:28640800-28646200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr22:28641000-28641200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr22:28641000-28641400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr22:28641000-28641400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr22:28641000-28641400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr22:28641000-28641400	Weak transcription	NHLF	lung
50	chr22:28641000-28642400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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