Variant report

Variant	rs13013824
Chromosome Location	chr2:85990667-85990668
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85981293..85984643-chr2:85987254..85991080,5	MCF-7	breast:
2	chr2:85988970..85991033-chr2:86009330..86011964,2	K562	blood:
3	chr2:85899004..85901888-chr2:85989811..85991933,2	MCF-7	breast:
4	chr2:85989736..85992227-chr2:85994375..85996424,2	K562	blood:
5	chr2:85985810..85988014-chr2:85988688..85991326,2	MCF-7	breast:
6	chr2:85989917..85993093-chr2:85993435..85996690,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168874	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12475263	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4832009	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4832011	0.86[AFR][1000 genomes]
rs4832195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832196	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719105	0.89[ASN][1000 genomes]
rs7558427	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	nsv874468	chr2:85926598-86001255	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1012593	chr2:85966323-85997189	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv874469	chr2:85973618-86025251	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv874470	chr2:85973618-86028257	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv874471	chr2:85976645-86021919	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription 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	1 gene(s)	inside rSNPs	diseases
6	nsv1001792	chr2:85983107-86016722	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv535805	chr2:85983107-86016722	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription 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	1 gene(s)	inside rSNPs	diseases
8	nsv535806	chr2:85990408-86007918	Enhancers Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85984200-85992000	Weak transcription	Fetal Kidney	kidney
2	chr2:85985400-85995200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:85986000-85990800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:85986000-85991200	Enhancers	Liver	Liver
5	chr2:85986000-85995800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:85986400-85995600	Weak transcription	Brain Angular Gyrus	brain
7	chr2:85986600-85991000	Weak transcription	Pancreas	Pancrea
8	chr2:85986600-85995000	Weak transcription	Esophagus	oesophagus
9	chr2:85986800-85991200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr2:85987000-85990800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:85987000-85991000	Weak transcription	NHLF	lung
12	chr2:85987000-85998400	Genic enhancers	Muscle Satellite Cultured Cells	--
13	chr2:85987200-85991000	Weak transcription	Brain Anterior Caudate	brain
14	chr2:85987200-85991200	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr2:85987200-85992200	Weak transcription	Colonic Mucosa	Colon
16	chr2:85987600-85991000	Enhancers	A549	lung
17	chr2:85988000-85991000	Enhancers	Primary B cells from cord blood	blood
18	chr2:85988000-85991200	Weak transcription	Osteobl	bone
19	chr2:85988000-85993000	Weak transcription	NHDF-Ad	bronchial
20	chr2:85988000-85996200	Enhancers	Hela-S3	cervix
21	chr2:85988200-85990800	Enhancers	Stomach Smooth Muscle	stomach
22	chr2:85988200-85991800	Weak transcription	HUVEC	blood vessel
23	chr2:85988400-85991000	Weak transcription	Lung	lung
24	chr2:85988400-85995000	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:85988600-85991200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr2:85988600-86000000	Enhancers	Right Atrium	heart
27	chr2:85988800-85991600	Weak transcription	Brain Substantia Nigra	brain
28	chr2:85989000-85991000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:85989000-85991200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:85989200-85991000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:85989200-85991000	Genic enhancers	HSMM	muscle
32	chr2:85989200-85991200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:85989200-85991200	Enhancers	Spleen	Spleen
34	chr2:85989200-85991600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:85989200-85991800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:85989200-85992200	Enhancers	HepG2	liver
37	chr2:85989400-85990800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:85989400-85991000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:85989400-85991000	Weak transcription	Ovary	ovary
40	chr2:85989400-85992600	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:85989400-85994800	Weak transcription	HSMMtube	muscle
42	chr2:85989600-85990800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:85989600-85990800	Weak transcription	Fetal Lung	lung
44	chr2:85989600-85991200	Enhancers	Left Ventricle	heart
45	chr2:85989600-85994200	Strong transcription	Gastric	stomach
46	chr2:85989800-85991400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:85989800-85992200	Weak transcription	Brain Germinal Matrix	brain
48	chr2:85989800-85993400	Weak transcription	Psoas Muscle	Psoas
49	chr2:85989800-85995200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:85990000-85990800	Weak transcription	Fetal Heart	heart

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