Variant report

Variant	rs56989102
Chromosome Location	chr2:171668946-171668947
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	CTCF	chr2:171668639-171669919	A549	lung:	n/a	chr2:171669437-171669447 chr2:171669434-171669452 chr2:171669429-171669450 chr2:171669440-171669449 chr2:171669435-171669451
2	CTCF	chr2:171668896-171669969	SK-N-SH	brain:	n/a	chr2:171669437-171669447 chr2:171669434-171669452 chr2:171669429-171669450 chr2:171669440-171669449 chr2:171669435-171669451

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:171254424..171255162-chr2:171668919..171669613,2	MCF-7	breast:

Variant related genes	Relation type
GAD1	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10168078	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1065651	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10930440	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11675773	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12463871	0.82[AMR][1000 genomes]
rs12464863	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12472397	0.81[AMR][1000 genomes]
rs12692960	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1362488	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1420378	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1420379	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1420380	0.81[AMR][1000 genomes]
rs1420381	0.81[AMR][1000 genomes]
rs17694562	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17694708	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17751035	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17751072	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17751234	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1894920	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1978340	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1990653	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2111000	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2216134	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2287110	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2287111	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2356234	0.81[AMR][1000 genomes]
rs2356236	0.85[EUR][1000 genomes]
rs2883888	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34137349	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34436957	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35127716	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35872782	0.81[AMR][1000 genomes]
rs3762553	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3762556	0.85[EUR][1000 genomes]
rs3791871	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3791872	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3791878	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4667657	0.81[AMR][1000 genomes]
rs4668315	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4668316	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55693618	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55804482	0.81[AMR][1000 genomes]
rs55923006	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56330225	0.81[AMR][1000 genomes]
rs56364811	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58919807	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62168369	0.81[AMR][1000 genomes]
rs62168370	0.81[AMR][1000 genomes]
rs62168371	0.82[AMR][1000 genomes]
rs62168373	0.82[AMR][1000 genomes]
rs62168376	0.82[AMR][1000 genomes]
rs62168396	0.82[AMR][1000 genomes]
rs62168397	0.81[AMR][1000 genomes]
rs62168399	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62168400	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62168401	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62168405	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62168409	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62168446	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62168447	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62168448	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62168454	0.83[ASN][1000 genomes]
rs6742220	0.81[AMR][1000 genomes]
rs6755814	0.97[ASN][1000 genomes]
rs6759584	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72887356	0.81[AMR][1000 genomes]
rs72887361	0.82[AMR][1000 genomes]
rs72887372	0.81[AMR][1000 genomes]
rs7568115	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7600585	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1806894	chr2:171651783-171679041	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171642400-171669000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:171666000-171669200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:171668600-171669600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:171668600-171670000	Active TSS	Brain Germinal Matrix	brain

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