Variant report

Variant	rs2622428
Chromosome Location	chr11:63905405-63905406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63859816..63862484-chr11:63904603..63906988,2	K562	blood:
2	chr11:63903545..63905452-chr11:63911377..63913056,2	MCF-7	breast:
3	chr11:63899428..63902376-chr11:63903166..63906655,5	MCF-7	breast:
4	chr11:63894281..63896174-chr11:63903272..63905656,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133315	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11549691	0.81[EUR][1000 genomes]
rs1544538	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs17851033	0.85[EUR][1000 genomes]
rs1938817	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070232	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2154984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2186571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2245837	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2622420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622422	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2622424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622430	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2701530	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2701536	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2701537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2701539	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4980504	1.00[YRI][hapmap]
rs4980506	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs583799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59250939	0.85[EUR][1000 genomes]
rs599549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs615924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
3	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
4	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv832184	chr11:63787702-63925084	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
7	nsv897659	chr11:63813470-63907079	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv832185	chr11:63819946-63963532	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
9	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
10	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
11	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
12	nsv356	chr11:63868847-63913129	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv897662	chr11:63889749-64150370	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
14	esv1801661	chr11:63894054-63937949	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2622428	PRDX5	Cis_1M	lymphoblastoid	RTeQTL
rs2622428	HSPC152	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63885600-63911200	Weak transcription	Gastric	stomach
2	chr11:63886800-63908600	Weak transcription	Ovary	ovary
3	chr11:63890600-63913600	Weak transcription	Esophagus	oesophagus
4	chr11:63892000-63915800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:63895800-63920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:63896600-63906600	Weak transcription	Spleen	Spleen
7	chr11:63896600-63909000	Weak transcription	Adipose Nuclei	Adipose
8	chr11:63897200-63918400	Weak transcription	Dnd41	blood
9	chr11:63898800-63916400	Weak transcription	Hela-S3	cervix
10	chr11:63900200-63931800	Weak transcription	Lung	lung
11	chr11:63900400-63905600	Weak transcription	Pancreas	Pancrea
12	chr11:63900400-63916000	Weak transcription	Fetal Intestine Large	intestine
13	chr11:63900800-63907600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:63900800-63916200	Weak transcription	Liver	Liver
15	chr11:63901000-63907800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:63901000-63908800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:63901200-63909000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr11:63901600-63908600	Weak transcription	HepG2	liver
19	chr11:63902000-63908200	Weak transcription	Aorta	Aorta
20	chr11:63902000-63916600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:63902800-63906600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr11:63902800-63915600	Weak transcription	Fetal Intestine Small	intestine
23	chr11:63903200-63905600	Weak transcription	Fetal Brain Female	brain
24	chr11:63903600-63915600	Weak transcription	Left Ventricle	heart
25	chr11:63903800-63905800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:63903800-63906800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:63904000-63906000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:63904000-63906000	Strong transcription	Right Ventricle	heart
29	chr11:63904000-63906800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:63904200-63908800	Weak transcription	Psoas Muscle	Psoas
31	chr11:63904200-63913400	Weak transcription	K562	blood
32	chr11:63904400-63905600	Weak transcription	Fetal Brain Male	brain
33	chr11:63904400-63905600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr11:63904400-63906000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr11:63904600-63905600	Weak transcription	Brain Germinal Matrix	brain
36	chr11:63904800-63908600	Weak transcription	Fetal Muscle Leg	muscle
37	chr11:63905200-63905800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr11:63905200-63905800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:63905400-63906000	Enhancers	Fetal Stomach	stomach

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