Variant report

Variant	rs1822293
Chromosome Location	chr11:10238974-10238975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10160763	0.92[ASN][1000 genomes]
rs10770100	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10840377	0.92[ASN][1000 genomes]
rs10840378	0.93[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11042615	1.00[CHB][hapmap]
rs11042632	1.00[CHB][hapmap]
rs11042641	1.00[CHB][hapmap]
rs11042682	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11042683	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs11042685	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1114426	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11600251	1.00[CHB][hapmap]
rs11606561	1.00[CHB][hapmap]
rs11607447	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12281432	1.00[ASW][hapmap];0.84[CEU][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.99[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12360783	1.00[CHB][hapmap]
rs12362060	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs12417184	1.00[CHB][hapmap]
rs12420122	0.92[ASN][1000 genomes]
rs1372809	0.85[CEU][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1372811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1442737	1.00[CHB][hapmap]
rs1442740	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1562782	1.00[ASW][hapmap];0.84[CEU][hapmap];0.85[CHD][hapmap]
rs17359113	1.00[CHB][hapmap]
rs1822291	0.92[ASN][1000 genomes]
rs1822292	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs1837978	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867135	0.92[ASN][1000 genomes]
rs1988724	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2044142	0.83[CHD][hapmap]
rs2083714	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2197170	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2197171	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs2218305	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2403291	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403292	1.00[CHB][hapmap]
rs2957657	0.83[CHD][hapmap]
rs35246982	0.83[ASN][1000 genomes]
rs35269701	0.92[ASN][1000 genomes]
rs35380986	0.83[ASN][1000 genomes]
rs4258371	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4281477	1.00[CHB][hapmap]
rs4385889	0.92[ASN][1000 genomes]
rs4430500	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4519084	0.92[ASN][1000 genomes]
rs4534577	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4550215	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4553358	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4612801	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4643073	0.92[ASN][1000 genomes]
rs4909923	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910095	1.00[CHB][hapmap]
rs4910100	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4910101	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910102	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910104	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4910108	0.81[YRI][hapmap]
rs4910109	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4910110	0.92[ASN][1000 genomes]
rs4910111	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs55796222	0.92[ASN][1000 genomes]
rs7110151	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs7117478	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7124401	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs716804	0.84[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7935774	0.92[ASN][1000 genomes]
rs7935934	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7937758	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7938491	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7948215	0.92[ASN][1000 genomes]
rs9645625	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv1039636	chr11:10126747-10280570	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1822293	SYT9	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10219000-10242200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:10227400-10240000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr11:10227600-10240200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:10227800-10239800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:10227800-10240000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr11:10227800-10242600	Weak transcription	Esophagus	oesophagus
7	chr11:10229600-10240200	Weak transcription	Fetal Stomach	stomach
8	chr11:10230200-10240000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:10230200-10240000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:10230200-10240200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr11:10230200-10240600	Weak transcription	A549	lung
12	chr11:10230600-10246800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:10231000-10240000	Weak transcription	Dnd41	blood
14	chr11:10231000-10240200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:10231000-10254400	Weak transcription	NHDF-Ad	bronchial
16	chr11:10231000-10254400	Weak transcription	NHLF	lung
17	chr11:10231200-10240000	Weak transcription	Fetal Intestine Small	intestine
18	chr11:10231400-10240200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:10231800-10240400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:10235400-10263400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr11:10237000-10240000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr11:10237200-10240200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr11:10237800-10243400	Weak transcription	HepG2	liver
24	chr11:10238800-10240200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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