Variant report

Variant	rs1456295
Chromosome Location	chr15:51979655-51979656
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51974117..51976857-chr15:51978812..51980643,2	MCF-7	breast:
2	chr15:51972403..51976508-chr15:51976780..51980487,4	K562	blood:
3	chr15:51964695..51967594-chr15:51978181..51980955,2	MCF-7	breast:
4	chr15:51974418..51976599-chr15:51979066..51980619,2	K562	blood:
5	chr15:51972908..51975133-chr15:51978339..51981508,3	MCF-7	breast:
6	chr15:51971642..51974295-chr15:51978244..51979923,2	K562	blood:
7	chr15:51978743..51984253-chr15:51984583..51988197,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104112	Chromatin interaction
ENSG00000259241	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1017679	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs10851501	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11070861	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12324531	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12441057	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12708427	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12901452	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12904173	0.90[CEU][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs12904583	0.83[EUR][1000 genomes]
rs1378892	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1378893	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1378894	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1378895	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1456297	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1471072	0.95[CEU][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1531157	0.88[EUR][1000 genomes]
rs1551657	0.81[EUR][1000 genomes]
rs17524750	0.83[EUR][1000 genomes]
rs17524906	0.95[CEU][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs1840707	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902595	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1902596	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2252220	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2305718	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2414112	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2606134	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606136	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606137	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606138	0.95[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606139	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606141	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2606143	0.95[CEU][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2606145	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606146	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2607110	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2607112	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2607116	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2607117	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]
rs2622768	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2622769	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2622770	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28408214	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28555597	0.86[MEX][hapmap]
rs3214015	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs34448759	0.83[EUR][1000 genomes]
rs34662965	0.81[EUR][1000 genomes]
rs34929849	0.82[EUR][1000 genomes]
rs35011964	0.84[EUR][1000 genomes]
rs4465557	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4774594	0.85[EUR][1000 genomes]
rs4775954	0.95[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55725532	0.83[EUR][1000 genomes]
rs60694229	0.84[AMR][1000 genomes]
rs6493507	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493511	0.95[CEU][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493512	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493514	1.00[CEU][hapmap];0.88[GIH][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs716986	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7180329	0.81[EUR][1000 genomes]
rs7181921	0.86[CEU][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8025974	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8027162	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8029731	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs897581	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs956171	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs9672605	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9944266	0.81[AMR][1000 genomes];0.84[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1456295	TMOD2	cis	parietal	SCAN
rs1456295	SCG3	cis	parietal	SCAN
rs1456295	ATP8B4	cis	parietal	SCAN
rs1456295	SCG3	cis	cerebellum	SCAN
rs1456295	BCL2L10	cis	parietal	SCAN
rs1456295	DMXL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:21 , 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	chr15:51974400-51983400	Weak transcription	Brain Hippocampus Middle	brain
3	chr15:51974400-51990800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:51974400-52005200	Weak transcription	Brain Anterior Caudate	brain
5	chr15:51974600-51983000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr15:51974600-51983200	Weak transcription	K562	blood
7	chr15:51974600-51984200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr15:51974600-51991000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:51974600-52016400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:51974800-51984600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:51975000-51980400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:51975000-51982600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:51975000-51993200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:51975200-51998400	Weak transcription	Brain Angular Gyrus	brain
15	chr15:51975600-51979800	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr15:51975600-52017200	Weak transcription	Fetal Brain Male	brain
17	chr15:51976800-51983200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:51978600-51990600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:51978800-51982200	Weak transcription	Fetal Brain Female	brain
20	chr15:51979200-51980200	Weak transcription	Brain Germinal Matrix	brain
21	chr15:51979600-51982000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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