Variant report

Variant	rs2607117
Chromosome Location	chr15:51985835-51985836
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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:51984106..51987260-chr15:51989301..51991929,3	MCF-7	breast:
2	chr15:51985262..51987318-chr15:51998907..52000749,2	K562	blood:
3	chr15:51984640..51986605-chr15:51992060..51993889,2	K562	blood:
4	chr15:51983304..51986110-chr15:51988118..51990669,2	MCF-7	breast:
5	chr15:51975005..51977651-chr15:51984880..51987418,3	K562	blood:
6	chr15:51985613..51987539-chr15:51999474..52001266,2	K562	blood:
7	chr15:51984283..51986352-chr15:51990636..51992962,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LYSMD2-2	chr15:51985413-51986134	ENSG00000259241.1

No data

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1017679	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11070861	0.81[EUR][1000 genomes]
rs12324531	0.84[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs12441057	0.81[EUR][1000 genomes]
rs12708427	0.81[EUR][1000 genomes]
rs12901452	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12904173	0.86[MEX][hapmap];0.91[TSI][hapmap]
rs1378892	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1378893	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1378894	0.83[EUR][1000 genomes]
rs1378895	0.83[EUR][1000 genomes]
rs1456295	0.84[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1456297	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1471072	0.84[CEU][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17524906	0.86[MEX][hapmap];0.90[TSI][hapmap]
rs1840707	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1902595	0.81[EUR][1000 genomes]
rs2252220	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs2305720	0.81[TSI][hapmap]
rs2414112	0.81[EUR][1000 genomes]
rs2606134	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2606136	0.84[CEU][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2606137	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2606138	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2606139	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2606141	0.85[EUR][1000 genomes]
rs2606143	0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs2606145	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2606146	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2607110	0.83[EUR][1000 genomes]
rs2607112	0.81[EUR][1000 genomes]
rs2607116	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2622768	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2622769	0.84[CEU][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2622770	0.84[CEU][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28555597	0.80[MEX][hapmap];0.81[TSI][hapmap]
rs4775954	0.91[TSI][hapmap]
rs6493511	0.86[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs6493512	0.81[EUR][1000 genomes]
rs6493514	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs716986	0.84[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7181921	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8025974	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8027162	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8029731	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs897581	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9672605	0.94[AMR][1000 genomes];0.90[EUR][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	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1035967	chr15:51949866-52008736	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2607117	SCG3	cis	cerebellum	SCAN
rs2607117	SCG3	cis	parietal	SCAN
rs2607117	TMOD2	cis	parietal	SCAN
rs2607117	ATP8B4	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51974200-52018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:51974400-51990800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr15:51974400-52005200	Weak transcription	Brain Anterior Caudate	brain
4	chr15:51974600-51991000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:51974600-52016400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:51975000-51993200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:51975200-51998400	Weak transcription	Brain Angular Gyrus	brain
8	chr15:51975600-52017200	Weak transcription	Fetal Brain Male	brain
9	chr15:51978600-51990600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:51980200-51988000	Strong transcription	Brain Germinal Matrix	brain
11	chr15:51982200-51996600	Strong transcription	Fetal Brain Female	brain
12	chr15:51983000-52013200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:51983400-51998400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr15:51983800-51990200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:51984400-51986000	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr15:51984400-51986800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:51984600-51986800	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:51984600-51991000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:51984600-51992600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:51984800-52018600	Weak transcription	Brain Hippocampus Middle	brain
21	chr15:51985000-51986800	Enhancers	K562	blood
22	chr15:51985400-51986200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:51985400-51992000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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