Variant report

Variant	rs13420559
Chromosome Location	chr2:11727264-11727265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr2:11726801-11727401	MCF-7	breast:	n/a	n/a
2	POLR2A	chr2:11726444-11727979	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:11727174-11727407	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:11727066-11727361	ProgFib	skin:	n/a	n/a
5	POLR2A	chr2:11712005-11732311	MCF-7	breast:	n/a	n/a
6	POLR2A	chr2:11726698-11727426	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:11725017-11728081	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
GREB1	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10183250	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11886664	1.00[EUR][1000 genomes]
rs11890221	1.00[EUR][1000 genomes]
rs11895768	1.00[EUR][1000 genomes]
rs13421766	1.00[EUR][1000 genomes]
rs13424731	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16857649	1.00[EUR][1000 genomes]
rs16857699	1.00[EUR][1000 genomes]
rs4668728	1.00[EUR][1000 genomes]
rs4669732	1.00[EUR][1000 genomes]
rs4669734	1.00[EUR][1000 genomes]
rs55736020	1.00[EUR][1000 genomes]
rs56273175	1.00[EUR][1000 genomes]
rs56352405	1.00[EUR][1000 genomes]
rs56820808	1.00[EUR][1000 genomes]
rs56834951	1.00[EUR][1000 genomes]
rs57251854	1.00[EUR][1000 genomes]
rs58477298	1.00[EUR][1000 genomes]
rs58686966	1.00[EUR][1000 genomes]
rs58819315	1.00[EUR][1000 genomes]
rs59157966	1.00[EUR][1000 genomes]
rs59416046	1.00[EUR][1000 genomes]
rs59554925	1.00[EUR][1000 genomes]
rs59836200	1.00[EUR][1000 genomes]
rs60798771	1.00[EUR][1000 genomes]
rs61091666	1.00[EUR][1000 genomes]
rs61358269	1.00[EUR][1000 genomes]
rs61382095	1.00[EUR][1000 genomes]
rs6432204	1.00[EUR][1000 genomes]
rs6432205	1.00[EUR][1000 genomes]
rs6432206	1.00[EUR][1000 genomes]
rs6710070	1.00[EUR][1000 genomes]
rs6712902	1.00[EUR][1000 genomes]
rs6745921	1.00[EUR][1000 genomes]
rs73185109	1.00[EUR][1000 genomes]
rs73915200	1.00[EUR][1000 genomes]
rs73915202	1.00[EUR][1000 genomes]
rs73917104	1.00[EUR][1000 genomes]
rs73917107	1.00[EUR][1000 genomes]
rs73917124	1.00[EUR][1000 genomes]
rs73917203	1.00[EUR][1000 genomes]
rs73917206	1.00[EUR][1000 genomes]
rs73917207	1.00[EUR][1000 genomes]
rs7559230	1.00[EUR][1000 genomes]
rs7562399	1.00[EUR][1000 genomes]
rs7565382	1.00[EUR][1000 genomes]
rs7585718	1.00[EUR][1000 genomes]
rs7598673	1.00[EUR][1000 genomes]
rs7602962	1.00[EUR][1000 genomes]
rs7608777	1.00[EUR][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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11694800-11755200	Weak transcription	Gastric	stomach
3	chr2:11700000-11767000	Weak transcription	Right Atrium	heart
4	chr2:11711600-11738600	Weak transcription	Left Ventricle	heart
5	chr2:11714400-11765000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:11717600-11767000	Weak transcription	Fetal Intestine Small	intestine
7	chr2:11719200-11738000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:11719400-11750800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:11720000-11735600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:11721600-11733000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:11723000-11740400	Weak transcription	Liver	Liver
12	chr2:11723200-11735400	Weak transcription	Brain Substantia Nigra	brain
13	chr2:11723400-11735200	Weak transcription	Fetal Lung	lung
14	chr2:11723400-11740000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:11723600-11735200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:11723600-11735600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:11723600-11738600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:11724200-11732800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:11724200-11732800	Weak transcription	Pancreas	Pancrea
20	chr2:11724400-11735200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:11724400-11735200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:11724400-11738000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:11724400-11738600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:11724400-11788600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:11724600-11732800	Strong transcription	HepG2	liver
26	chr2:11724600-11735400	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:11724600-11741000	Weak transcription	Brain Anterior Caudate	brain
28	chr2:11724600-11766800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:11724600-11766800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:11724800-11735400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:11724800-11735600	Weak transcription	Brain Angular Gyrus	brain
32	chr2:11724800-11736000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:11724800-11749600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:11725000-11743800	Weak transcription	Fetal Kidney	kidney
35	chr2:11725200-11730200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:11725200-11730600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr2:11725400-11728200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:11725400-11742400	Strong transcription	Ovary	ovary
39	chr2:11725600-11766800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:11725800-11727600	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr2:11725800-11728600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:11725800-11729400	Strong transcription	Fetal Muscle Leg	muscle
43	chr2:11725800-11730800	Strong transcription	Fetal Stomach	stomach
44	chr2:11726600-11728400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:11726600-11735400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:11727200-11727600	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:11727200-11733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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