Variant report

Variant	rs134507
Chromosome Location	chr22:28753833-28753834
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28745543..28747734-chr22:28752651..28754673,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1303845	1.00[CEU][hapmap];0.92[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs134179	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap]
rs134180	1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs134183	0.95[CEU][hapmap]
rs134196	0.92[JPT][hapmap]
rs134489	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs134500	1.00[CEU][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs134526	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs134541	1.00[CEU][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs134543	1.00[CEU][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes]
rs134548	1.00[CEU][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs134551	0.92[JPT][hapmap]
rs17503350	0.95[CEU][hapmap]
rs2346397	0.92[JPT][hapmap]
rs5752743	0.95[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs5762629	0.83[CEU][hapmap]
rs5762660	0.90[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs5762680	0.83[CEU][hapmap]
rs695439	0.81[EUR][1000 genomes]
rs695591	1.00[CEU][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs695625	1.00[CEU][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs7284814	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs8140229	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][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
rs134507	SUSD2	cis	parietal	SCAN
rs134507	TTC28	cis	cerebellum	SCAN
rs134507	SEC14L4	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28741600-28759000	Weak transcription	Fetal Stomach	stomach
2	chr22:28742800-28759600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr22:28743000-28759000	Weak transcription	Dnd41	blood
4	chr22:28745200-28754400	Weak transcription	Brain Anterior Caudate	brain
5	chr22:28746200-28754200	Weak transcription	Fetal Heart	heart
6	chr22:28748000-28755800	Weak transcription	Fetal Intestine Small	intestine
7	chr22:28748000-28759600	Weak transcription	Fetal Lung	lung
8	chr22:28748200-28754200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr22:28748800-28754200	Weak transcription	Fetal Brain Male	brain
10	chr22:28752000-28754400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:28752400-28754000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr22:28752800-28754200	Weak transcription	Right Ventricle	heart
13	chr22:28752800-28759000	Weak transcription	Ovary	ovary
14	chr22:28752800-28768600	Weak transcription	Left Ventricle	heart
15	chr22:28753200-28755000	Enhancers	Brain Germinal Matrix	brain
16	chr22:28753800-28754000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr22:28753800-28754400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr22:28753800-28754800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr22:28753800-28754800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr22:28753800-28754800	Enhancers	Fetal Brain Female	brain
21	chr22:28753800-28755000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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