Variant report

Variant	rs639406
Chromosome Location	chr11:63889749-63889750
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr11:63888962-63889890	SK-N-SH	brain:	n/a	n/a
2	YY1	chr11:63889546-63889842	SK-N-SH_RA	brain:	n/a	chr11:63889701-63889711
3	YY1	chr11:63889456-63889931	SK-N-SH	brain:	n/a	chr11:63889864-63889883 chr11:63889701-63889711 chr11:63889871-63889881
4	RCOR1	chr11:63888285-63890056	IMR90	lung:	n/a	n/a
5	MEF2A	chr11:63888925-63889875	SK-N-SH	brain:	n/a	chr11:63889583-63889604 chr11:63889588-63889602 chr11:63889329-63889340 chr11:63889590-63889599 chr11:63889587-63889603 chr11:63889587-63889602 chr11:63889589-63889600 chr11:63889583-63889604 chr11:63889583-63889604
6	POLR2A	chr11:63889732-63889864	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr11:63889639-63889792	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chr11:63889504-63890021	H1-hESC	embryonic stem cell:	n/a	chr11:63889864-63889883 chr11:63889701-63889711 chr11:63889871-63889881
9	MAX	chr11:63889588-63890113	H1-hESC	embryonic stem cell:	n/a	n/a
10	FOSL2	chr11:63888962-63889936	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr11:63888971-63889901	SK-N-SH	brain:	n/a	n/a
12	MXI1	chr11:63888706-63889912	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:63888452..63890195-chr11:63909642..63911388,2	K562	blood:
2	chr11:63889039..63891397-chr11:63901095..63904442,4	K562	blood:
3	chr11:63888646..63891541-chr11:63955037..63956555,2	MCF-7	breast:
4	chr11:63888929..63891222-chr11:63896109..63898759,2	MCF-7	breast:
5	chr11:63889514..63891189-chr11:63902190..63904442,3	K562	blood:

Variant related genes	Relation type
ENSG00000256341	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

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[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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	0.85[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];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2186571	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[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];0.88[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622428	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	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2701530	0.88[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];0.88[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];0.88[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs615924	0.88[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];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688241	0.88[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	nsv897658	chr11:63810944-63897759	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription 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	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
9	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
10	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
11	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
12	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
13	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
14	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs639406	PRDX5	Cis_1M	lymphoblastoid	RTeQTL
rs639406	TRMT112	cis	lymphoblastoid	seeQTL
rs639406	HSPC152	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63875400-63896200	Weak transcription	Spleen	Spleen
2	chr11:63879600-63890200	Weak transcription	Liver	Liver
3	chr11:63879800-63891600	Weak transcription	Primary T cells from cord blood	blood
4	chr11:63881800-63891800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:63882200-63892800	Weak transcription	Fetal Kidney	kidney
6	chr11:63883000-63890800	Weak transcription	Dnd41	blood
7	chr11:63884600-63889800	Weak transcription	Pancreas	Pancrea
8	chr11:63885000-63896600	Weak transcription	Hela-S3	cervix
9	chr11:63885400-63892400	Weak transcription	Fetal Intestine Small	intestine
10	chr11:63885400-63898600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr11:63885600-63911200	Weak transcription	Gastric	stomach
12	chr11:63886000-63891000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:63886000-63891200	Enhancers	Fetal Brain Male	brain
14	chr11:63886200-63890800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:63886200-63890800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:63886800-63908600	Weak transcription	Ovary	ovary
17	chr11:63887200-63892000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr11:63887400-63890800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr11:63887600-63890800	Enhancers	Brain Cingulate Gyrus	brain
20	chr11:63887800-63890400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr11:63887800-63891000	Enhancers	Brain Germinal Matrix	brain
22	chr11:63888000-63890400	Enhancers	HMEC	breast
23	chr11:63888000-63890800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr11:63888000-63891000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:63888000-63891800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr11:63888000-63891800	Enhancers	Fetal Muscle Leg	muscle
27	chr11:63888200-63890000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:63888200-63890000	Enhancers	Brain Angular Gyrus	brain
29	chr11:63888200-63890200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:63888200-63890400	Enhancers	HSMMtube	muscle
31	chr11:63888200-63890600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:63888200-63890600	Enhancers	HSMM	muscle
33	chr11:63888200-63890800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:63888200-63890800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:63888200-63891600	Enhancers	Brain Anterior Caudate	brain
36	chr11:63888200-63891800	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr11:63888200-63892000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr11:63888200-63894000	Enhancers	Fetal Thymus	thymus
39	chr11:63888400-63889800	Enhancers	Fetal Stomach	stomach
40	chr11:63888400-63890000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:63888400-63890200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:63888400-63890200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr11:63888400-63890400	Enhancers	H1 Cell Line	embryonic stem cell
44	chr11:63888400-63890400	Enhancers	H9 Cell Line	embryonic stem cell
45	chr11:63888400-63890600	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr11:63888400-63890600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:63888400-63890800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr11:63888400-63890800	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr11:63888400-63890800	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr11:63888400-63890800	Enhancers	Brain Hippocampus Middle	brain

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