Variant report

Variant	rs11886523
Chromosome Location	chr2:100886655-100886656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:100877002..100888885-chr2:100934823..100940762,23	MCF-7	breast:
2	chr2:100885913..100887573-chr2:100900551..100902745,2	MCF-7	breast:
3	chr2:100882860..100889379-chr2:100906197..100910186,11	MCF-7	breast:
4	chr2:100885071..100887270-chr2:100902977..100904501,2	MCF-7	breast:
5	chr2:100884594..100887131-chr2:100887160..100889077,2	MCF-7	breast:
6	chr2:100883299..100887347-chr2:100906337..100908618,4	MCF-7	breast:
7	chr2:100881955..100884810-chr2:100886206..100888187,2	K562	blood:
8	chr2:100885390..100890009-chr2:100935265..100941023,7	MCF-7	breast:
9	chr2:100886067..100888697-chr2:100889911..100892132,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10170878	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10173499	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12463633	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12464433	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12464505	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12467008	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12472141	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13394110	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13397010	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13397337	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2871341	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34044131	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4851281	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851282	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55856206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57328601	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60501704	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62148117	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62148118	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707358	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6724490	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6727712	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72821119	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72821120	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72821122	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72821124	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72821125	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72821126	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72821130	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72821133	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100874600-100891400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:100877600-100888600	Weak transcription	Ovary	ovary
3	chr2:100879000-100887000	Weak transcription	Gastric	stomach
4	chr2:100879400-100891200	Weak transcription	Brain Anterior Caudate	brain
5	chr2:100879400-100896200	Weak transcription	Spleen	Spleen
6	chr2:100879400-100900200	Weak transcription	Brain Substantia Nigra	brain
7	chr2:100880000-100891400	Weak transcription	Brain Germinal Matrix	brain
8	chr2:100880200-100898400	Weak transcription	A549	lung
9	chr2:100881000-100887400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:100881000-100887600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:100881800-100887200	Weak transcription	K562	blood
12	chr2:100882000-100887400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:100884200-100900200	Weak transcription	Brain Angular Gyrus	brain
14	chr2:100884600-100887000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:100884800-100897400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:100885400-100891200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:100885600-100887200	Enhancers	Fetal Intestine Small	intestine
18	chr2:100885600-100898200	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:100885600-100902000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:100885800-100887000	Enhancers	Fetal Intestine Large	intestine
21	chr2:100885800-100887200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:100886000-100886800	Enhancers	HepG2	liver
23	chr2:100886000-100887200	Weak transcription	Placenta	Placenta
24	chr2:100886000-100891200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr2:100886400-100886800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:100886400-100887000	Enhancers	Adipose Nuclei	Adipose
27	chr2:100886400-100891000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr2:100886600-100887600	Enhancers	Pancreas	Pancrea

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