Variant report

Variant	rs561886
Chromosome Location	chr11:94397663-94397664
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:94393858..94398288-chr11:94398504..94402115,4	K562	blood:
2	chr11:94396012..94398288-chr11:94399899..94402115,2	K562	blood:
3	chr11:94390356..94393073-chr11:94395941..94399822,3	K562	blood:
4	chr11:94389844..94391856-chr11:94396881..94399230,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10765692	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10831261	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10831264	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11020892	0.80[EUR][1000 genomes]
rs12285867	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12362413	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12362437	0.91[CEU][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12364020	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12365249	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12365323	0.91[CEU][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16920846	0.87[CHB][hapmap]
rs17607689	0.80[EUR][1000 genomes]
rs2509341	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4127395	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4127396	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4127397	0.87[CHB][hapmap]
rs487078	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501785	0.87[CHB][hapmap]
rs506926	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56412399	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs567300	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs584225	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586026	0.95[AFR][1000 genomes]
rs60917421	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs674106	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677244	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677331	0.86[CHB][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679928	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7104326	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7110345	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7115977	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7119223	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7130432	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7131489	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73522217	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7927928	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7931634	0.91[CEU][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3356576	chr11:94396904-94400502	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs561886	SESN3	cis	cerebellum	SCAN
rs561886	CRYL1	trans	lymphoblastoid	seeQTL
rs561886	SESN3	cis	parietal	SCAN
rs561886	SNORA1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:94384600-94404600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:94391000-94404600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:94392200-94398000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:94395400-94410800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:94395800-94399200	Enhancers	Placenta	Placenta
6	chr11:94396000-94404600	Weak transcription	Gastric	stomach
7	chr11:94396400-94397800	Genic enhancers	H9 Cell Line	embryonic stem cell
8	chr11:94396400-94397800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:94396400-94398800	Enhancers	Hela-S3	cervix
10	chr11:94396400-94404600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:94396800-94398600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:94396800-94400600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr11:94397000-94398000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:94397000-94400000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:94397000-94400400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:94397400-94398000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:94397400-94398000	Enhancers	HMEC	breast
18	chr11:94397400-94398000	Enhancers	NHEK	skin
19	chr11:94397400-94398200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:94397400-94398600	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr11:94397600-94397800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:94397600-94397800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr11:94397600-94397800	Enhancers	Esophagus	oesophagus
24	chr11:94397600-94398000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
25	chr11:94397600-94398000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:94397600-94398000	Enhancers	Fetal Muscle Leg	muscle
27	chr11:94397600-94398000	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr11:94397600-94398800	Enhancers	Fetal Intestine Large	intestine
29	chr11:94397600-94398800	Enhancers	Pancreas	Pancrea
30	chr11:94397600-94399200	Enhancers	Fetal Intestine Small	intestine

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