Variant report

Variant	rs2701530
Chromosome Location	chr11:63923377-63923378
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63921279..63924058-chr11:63951679..63954270,3	K562	blood:
2	chr11:63918153..63920465-chr11:63921554..63923972,2	MCF-7	breast:
3	chr11:63921851..63923670-chr11:63924013..63926369,2	MCF-7	breast:
4	chr11:63920929..63923512-chr11:63957225..63959261,2	MCF-7	breast:
5	chr11:63923167..63927304-chr11:63949302..63952377,3	MCF-7	breast:
6	chr11:63922444..63925519-chr11:63951476..63954274,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168439	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11549691	0.85[EUR][1000 genomes]
rs1544538	0.89[EUR][1000 genomes]
rs17851033	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1938817	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2070232	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2154984	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2186571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245837	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2622420	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2622422	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2622424	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2622428	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2622430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2701536	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2701537	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2701539	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4980506	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs583799	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59250939	0.89[EUR][1000 genomes]
rs599549	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs615924	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs616652	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs639406	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs688241	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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	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
8	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
9	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
10	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
11	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
12	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
13	nsv897663	chr11:63910153-63962152	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	86 gene(s)	inside rSNPs	n/a
14	nsv897664	chr11:63919742-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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	237 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2701530	PRDX5	Cis_1M	lymphoblastoid	RTeQTL
rs2701530	HSPC152	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63900200-63931800	Weak transcription	Lung	lung
2	chr11:63911600-63932600	Weak transcription	Primary T cells from cord blood	blood
3	chr11:63916200-63924200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr11:63916200-63932000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr11:63916400-63932000	Weak transcription	Stomach Mucosa	stomach
6	chr11:63916600-63932200	Weak transcription	Fetal Intestine Large	intestine
7	chr11:63918200-63932200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr11:63918600-63931800	Weak transcription	Gastric	stomach
9	chr11:63919000-63923800	Weak transcription	Left Ventricle	heart
10	chr11:63919000-63932000	Weak transcription	Adipose Nuclei	Adipose
11	chr11:63919200-63924000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr11:63919200-63928800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:63920000-63925600	Weak transcription	Fetal Intestine Small	intestine
14	chr11:63920200-63931800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:63920600-63923800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr11:63920600-63924200	Weak transcription	Pancreas	Pancrea
17	chr11:63920600-63925000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:63920600-63925400	Weak transcription	Psoas Muscle	Psoas
19	chr11:63920600-63928600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr11:63920600-63928800	Weak transcription	Aorta	Aorta
21	chr11:63920600-63931800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:63920600-63931800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr11:63920600-63932200	Weak transcription	Brain Substantia Nigra	brain
24	chr11:63920600-63932200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr11:63920600-63932400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:63920600-63932400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:63920800-63925600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:63920800-63931800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr11:63920800-63931800	Weak transcription	Liver	Liver
30	chr11:63920800-63931800	Weak transcription	Colonic Mucosa	Colon
31	chr11:63920800-63932000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:63921000-63923800	Weak transcription	Brain Anterior Caudate	brain
33	chr11:63921000-63924000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr11:63921000-63924000	Weak transcription	Brain Hippocampus Middle	brain
35	chr11:63921000-63925400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:63921000-63931600	Weak transcription	Dnd41	blood
37	chr11:63921000-63931800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr11:63921000-63932000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr11:63921000-63932200	Weak transcription	Small Intestine	intestine
40	chr11:63921000-63932400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:63921000-63932400	Weak transcription	A549	lung
42	chr11:63921200-63927200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:63921400-63923800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:63921400-63932200	Weak transcription	Esophagus	oesophagus
45	chr11:63921600-63923600	Weak transcription	Fetal Stomach	stomach
46	chr11:63921600-63924200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:63921600-63924400	Weak transcription	Hela-S3	cervix
48	chr11:63921600-63925200	Weak transcription	Right Ventricle	heart
49	chr11:63921600-63929600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr11:63921800-63923800	Weak transcription	Fetal Heart	heart

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