Variant report

Variant	rs551334
Chromosome Location	chr22:27609597-27609598
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	chr22:27602742..27604550-chr22:27607695..27610449,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CRYBA4-13	chr22:27609476-27609693	expReg_chr22_1575_+

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11090478	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2342399	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2342400	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2342401	0.84[AMR][1000 genomes]
rs3888463	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs565638	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs572784	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8135373	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9306437	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9613397	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9613399	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917333	chr22:26931825-27692024	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	142 gene(s)	inside rSNPs	diseases
2	esv34168	chr22:27289097-27678031	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3413125	chr22:27404463-28121577	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv459860	chr22:27527005-28181436	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv588872	chr22:27527005-28181436	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1064910	chr22:27609597-27648408	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs551334	YPEL1	cis	cerebellum	SCAN
rs551334	HPS4	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27603000-27609600	Weak transcription	Aorta	Aorta
2	chr22:27605400-27610000	Enhancers	Placenta Amnion	Placenta Amnion
3	chr22:27606400-27610200	Enhancers	Fetal Intestine Small	intestine
4	chr22:27606600-27610000	Weak transcription	Brain Germinal Matrix	brain
5	chr22:27606800-27620000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr22:27607000-27611400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr22:27607200-27609600	Enhancers	Colon Smooth Muscle	Colon
8	chr22:27607200-27610400	Enhancers	Fetal Intestine Large	intestine
9	chr22:27607600-27610200	Enhancers	Rectal Smooth Muscle	rectum
10	chr22:27607600-27611400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr22:27608000-27610000	Enhancers	Placenta	Placenta
12	chr22:27608000-27611600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr22:27608000-27611600	Enhancers	Osteobl	bone
14	chr22:27608000-27611800	Enhancers	Adipose Nuclei	Adipose
15	chr22:27608200-27609600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:27608200-27609600	Enhancers	HSMM	muscle
17	chr22:27608200-27610000	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr22:27608200-27610400	Enhancers	NH-A	brain
19	chr22:27608200-27611000	Enhancers	Fetal Muscle Leg	muscle
20	chr22:27608200-27611200	Enhancers	Spleen	Spleen
21	chr22:27608200-27611600	Enhancers	Ovary	ovary
22	chr22:27608200-27611800	Enhancers	Fetal Stomach	stomach
23	chr22:27608400-27609600	Enhancers	Duodenum Mucosa	Duodenum
24	chr22:27608600-27609600	Enhancers	Stomach Mucosa	stomach
25	chr22:27608600-27611000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr22:27608600-27611200	Enhancers	Stomach Smooth Muscle	stomach
27	chr22:27608600-27612200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr22:27608800-27609600	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr22:27608800-27609800	Enhancers	Left Ventricle	heart
30	chr22:27608800-27609800	Enhancers	Right Ventricle	heart
31	chr22:27608800-27610000	Enhancers	Right Atrium	heart
32	chr22:27608800-27610200	Bivalent Enhancer	Fetal Kidney	kidney
33	chr22:27608800-27611200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr22:27608800-27612800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr22:27609000-27610200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
36	chr22:27609000-27610400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr22:27609200-27609800	Enhancers	HUVEC	blood vessel
38	chr22:27609200-27610000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
39	chr22:27609200-27615800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr22:27609400-27610000	Weak transcription	Fetal Lung	lung
41	chr22:27609400-27611000	Enhancers	Lung	lung
42	chr22:27609400-27611200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr22:27609400-27613000	Weak transcription	A549	lung

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