Variant report

Variant	rs134173
Chromosome Location	chr22:28618454-28618455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs134176	0.94[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs134177	0.94[ASN][1000 genomes]
rs134178	0.85[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs134193	0.95[ASN][1000 genomes]
rs4822954	0.90[ASN][1000 genomes]
rs5762553	0.87[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.88[ASN][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	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
rs134173	TTC28	cis	cerebellum	SCAN
rs134173	RASL10A	cis	parietal	SCAN
rs134173	SUSD2	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28612200-28625600	Weak transcription	Aorta	Aorta
2	chr22:28612200-28634800	Weak transcription	Dnd41	blood
3	chr22:28613800-28618800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr22:28615800-28626400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr22:28616600-28620400	Weak transcription	Fetal Brain Male	brain
6	chr22:28617000-28620000	Weak transcription	Left Ventricle	heart
7	chr22:28617400-28619000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr22:28617400-28625400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr22:28617600-28626200	Weak transcription	Psoas Muscle	Psoas
10	chr22:28617800-28620000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr22:28617800-28620000	Weak transcription	Right Atrium	heart
12	chr22:28617800-28620200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr22:28617800-28620200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr22:28617800-28620800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr22:28618000-28619000	Enhancers	Colon Smooth Muscle	Colon
16	chr22:28618000-28619400	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr22:28618000-28619400	Enhancers	Fetal Muscle Leg	muscle
18	chr22:28618000-28620400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr22:28618000-28620400	Enhancers	NHDF-Ad	bronchial
20	chr22:28618000-28620400	Enhancers	NHLF	lung
21	chr22:28618000-28620600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr22:28618200-28618800	Weak transcription	NH-A	brain
23	chr22:28618200-28619200	Enhancers	Fetal Lung	lung
24	chr22:28618200-28620400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr22:28618200-28620400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr22:28618400-28618800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr22:28618400-28619200	Enhancers	Fetal Brain Female	brain
28	chr22:28618400-28619400	Enhancers	Brain Cingulate Gyrus	brain
29	chr22:28618400-28619400	Enhancers	Brain Hippocampus Middle	brain
30	chr22:28618400-28620400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr22:28618400-28626800	Weak transcription	Fetal Kidney	kidney
32	chr22:28618400-28639600	Weak transcription	Ovary	ovary
33	chr22:28618400-28662200	Weak transcription	Pancreas	Pancrea

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