Variant report

Variant	rs11677111
Chromosome Location	chr2:77747669-77747670
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:77747263..77749621-chr20:52208634..52211022,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171940	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11685687	1.00[CEU][hapmap]
rs11689077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690363	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695329	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17014228	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861073	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62159464	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62159465	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62159467	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62159469	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62159470	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62162645	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597037	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874333	chr2:77315349-77798886	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv518504	chr2:77326832-78172786	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1004938	chr2:77347740-78186543	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535783	chr2:77347740-78186543	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv529904	chr2:77347741-78186542	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv997329	chr2:77354560-78176285	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv874339	chr2:77683562-77872197	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv874340	chr2:77730014-77786509	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11677111	PRDX2	trans	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:77742200-77749600	Active TSS	Brain Angular Gyrus	brain
2	chr2:77744000-77749800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr2:77744000-77749800	Active TSS	Fetal Brain Female	brain
4	chr2:77745200-77749600	Active TSS	Brain Anterior Caudate	brain
5	chr2:77745400-77749400	Active TSS	Brain Cingulate Gyrus	brain
6	chr2:77745600-77749600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:77746000-77747800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr2:77746200-77749600	Active TSS	Brain Hippocampus Middle	brain
9	chr2:77746400-77748200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:77746600-77748600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:77746600-77749600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:77746600-77749600	Active TSS	Brain Substantia Nigra	brain
13	chr2:77746800-77747800	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr2:77747000-77748600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr2:77747000-77748600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr2:77747000-77749200	Active TSS	Fetal Muscle Leg	muscle
17	chr2:77747000-77749400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr2:77747000-77749600	Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr2:77747200-77748200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:77747200-77748200	Active TSS	Fetal Stomach	stomach
21	chr2:77747200-77748600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr2:77747200-77748600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr2:77747200-77748600	Active TSS	Stomach Smooth Muscle	stomach
24	chr2:77747400-77748000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
25	chr2:77747400-77748000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr2:77747400-77748000	Flanking Active TSS	Fetal Lung	lung
27	chr2:77747400-77748400	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr2:77747400-77748600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:77747400-77749400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr2:77747600-77747800	Flanking Active TSS	Liver	Liver
31	chr2:77747600-77747800	Flanking Active TSS	Fetal Heart	heart
32	chr2:77747600-77747800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
33	chr2:77747600-77747800	Flanking Active TSS	NHLF	lung
34	chr2:77747600-77748000	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr2:77747600-77748000	Flanking Active TSS	Fetal Brain Male	brain
36	chr2:77747600-77748000	Enhancers	Right Ventricle	heart
37	chr2:77747600-77748200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:77747600-77748200	Enhancers	Fetal Kidney	kidney
39	chr2:77747600-77748600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:77747600-77749200	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr2:77747600-77749400	Active TSS	H9 Cell Line	embryonic stem cell
42	chr2:77747600-77749400	Active TSS	Adipose Nuclei	Adipose

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