Variant report

Variant	rs61362255
Chromosome Location	chr2:11654874-11654875
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	EP300	chr2:11654348-11655011	HepG2	liver:	n/a	n/a
2	MYBL2	chr2:11653801-11654939	HepG2	liver:	n/a	n/a
3	FOXA1	chr2:11654068-11654976	HepG2	liver:	n/a	n/a
4	FOXA2	chr2:11653903-11655142	HepG2	liver:	n/a	n/a
5	HNF4A	chr2:11654506-11654918	HepG2	liver:	n/a	chr2:11654731-11654743
6	FOXA1	chr2:11654122-11654885	HepG2	liver:	n/a	n/a
7	TEAD4	chr2:11654127-11654993	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RNA5SP84	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10169987	0.86[ASN][1000 genomes]
rs10174895	0.86[ASN][1000 genomes]
rs10192123	0.86[ASN][1000 genomes]
rs10201673	0.86[ASN][1000 genomes]
rs10205078	0.86[ASN][1000 genomes]
rs10929750	0.86[ASN][1000 genomes]
rs11897533	0.86[ASN][1000 genomes]
rs13383410	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13388093	0.86[ASN][1000 genomes]
rs13395155	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407457	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407702	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13418262	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13424905	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430148	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432124	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13432756	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16857565	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002730	0.86[ASN][1000 genomes]
rs2043542	0.86[ASN][1000 genomes]
rs2082829	0.86[ASN][1000 genomes]
rs2082830	0.86[ASN][1000 genomes]
rs4668729	0.86[ASN][1000 genomes]
rs4669737	0.86[ASN][1000 genomes]
rs4669739	0.86[ASN][1000 genomes]
rs4669740	0.86[ASN][1000 genomes]
rs6432209	0.86[ASN][1000 genomes]
rs6719003	0.86[ASN][1000 genomes]
rs6719009	0.86[ASN][1000 genomes]
rs6739168	0.86[ASN][1000 genomes]
rs6741736	0.86[ASN][1000 genomes]
rs6756327	0.86[ASN][1000 genomes]
rs73187472	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580473	0.99[EUR][1000 genomes]
rs7597108	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875231	0.86[ASN][1000 genomes]
rs877164	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11639600-11655000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:11647000-11664400	Weak transcription	Right Ventricle	heart
3	chr2:11647000-11665800	Weak transcription	Right Atrium	heart
4	chr2:11648800-11655200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:11648800-11655600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:11648800-11655600	Weak transcription	Fetal Stomach	stomach
7	chr2:11649000-11655400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:11651000-11655800	Enhancers	HepG2	liver
9	chr2:11651200-11658200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:11651400-11655400	Enhancers	H9 Cell Line	embryonic stem cell
11	chr2:11651400-11657000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:11652000-11655000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:11652600-11655400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:11652600-11656200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr2:11652600-11656400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:11653200-11656200	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr2:11653200-11656600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:11653400-11657400	Enhancers	Ovary	ovary
19	chr2:11653600-11656000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr2:11653600-11656000	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr2:11653800-11655000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:11654000-11656600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:11654000-11664000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:11654200-11655200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:11654400-11656800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:11654600-11655600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:11654800-11655400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:11654800-11664400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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