Variant report

Variant	rs2701539
Chromosome Location	chr11:63963378-63963379
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:63963231-63963603	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:63963030-63963691	PFSK-1	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:63962580..63965391-chr11:63991959..63994483,2	MCF-7	breast:
2	chr11:63961712..63963731-chr11:63963830..63966290,2	K562	blood:
3	chr11:63962555..63965577-chr11:63969576..63973064,3	MCF-7	breast:
4	chr11:63962304..63965510-chr11:64012798..64015195,3	MCF-7	breast:
5	chr11:63951087..63956474-chr11:63963164..63967847,7	MCF-7	breast:
6	chr11:63932754..63935809-chr11:63963316..63968184,5	MCF-7	breast:

No data

Variant related genes	Relation type
STIP1	TF binding region
ENSG00000168439	Chromatin interaction
ENSG00000173457	Chromatin interaction
ENSG00000149743	Chromatin interaction
ENSG00000256940	Chromatin interaction
ENSG00000133315	Chromatin interaction
ENSG00000149761	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11549691	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1544538	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17851033	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938817	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2070232	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154984	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2186571	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2245837	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2622420	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2622422	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2622424	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2622428	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2622430	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2701530	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2701536	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2701537	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28395880	0.84[AMR][1000 genomes]
rs4980506	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs583799	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59250939	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs599549	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs615924	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs616652	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs639406	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs688241	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv468592	chr11:63924446-64042997	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
12	nsv555184	chr11:63924446-64042997	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
13	nsv897665	chr11:63927695-64026144	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	155 gene(s)	inside rSNPs	diseases
14	nsv897666	chr11:63929493-64026144	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	155 gene(s)	inside rSNPs	diseases
15	nsv869944	chr11:63932152-64123062	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
16	nsv468593	chr11:63941734-64089874	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
17	nsv555185	chr11:63941734-64089874	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
18	nsv555186	chr11:63949095-64097233	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
19	nsv468595	chr11:63953121-64027888	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases
20	nsv555187	chr11:63953121-64027888	Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2701539	PRDX5	Cis_1M	lymphoblastoid	RTeQTL
rs2701539	HSPC152	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63954600-63967400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:63955000-63969400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:63955200-63971600	Strong transcription	Fetal Intestine Small	intestine
4	chr11:63955200-63974400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:63955200-63975000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr11:63955200-63975200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:63955800-63971200	Strong transcription	Fetal Stomach	stomach
8	chr11:63955800-63975400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:63956000-63973600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:63956200-63964000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:63956200-63974200	Weak transcription	Right Atrium	heart
12	chr11:63956400-63970200	Weak transcription	Stomach Mucosa	stomach
13	chr11:63957000-63970600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:63957000-63971200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:63957000-63971400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr11:63957200-63965800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:63957400-63964800	Weak transcription	Fetal Heart	heart
18	chr11:63957400-63971000	Strong transcription	Dnd41	blood
19	chr11:63957400-63972000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr11:63957400-63974800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:63957400-63975800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:63957600-63970400	Strong transcription	Fetal Thymus	thymus
23	chr11:63958200-63971200	Strong transcription	Hela-S3	cervix
24	chr11:63959200-63972200	Strong transcription	Lung	lung
25	chr11:63959400-63964000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:63959400-63966000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr11:63959400-63971600	Strong transcription	Placenta	Placenta
28	chr11:63959400-63972000	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr11:63959400-63972000	Strong transcription	Thymus	Thymus
30	chr11:63959600-63966400	Strong transcription	Ovary	ovary
31	chr11:63959600-63966400	Strong transcription	HSMM	muscle
32	chr11:63959600-63971400	Strong transcription	A549	lung
33	chr11:63959600-63975000	Strong transcription	NHEK	skin
34	chr11:63959600-63976000	Strong transcription	Fetal Brain Female	brain
35	chr11:63959600-63977000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr11:63959800-63965800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr11:63959800-63966200	Strong transcription	K562	blood
38	chr11:63959800-63966400	Strong transcription	NHLF	lung
39	chr11:63959800-63967800	Strong transcription	Liver	Liver
40	chr11:63959800-63971000	Strong transcription	GM12878-XiMat	blood
41	chr11:63959800-63971600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
42	chr11:63959800-63971600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:63959800-63971600	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr11:63959800-63971600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:63959800-63971800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr11:63959800-63971800	Strong transcription	Primary T cells from cord blood	blood
47	chr11:63959800-63971800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr11:63959800-63971800	Strong transcription	Adipose Nuclei	Adipose
49	chr11:63959800-63971800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr11:63959800-63971800	Strong transcription	Stomach Smooth Muscle	stomach

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