Variant report

Variant	rs2251275
Chromosome Location	chr15:83560575-83560576
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83558429..83560638-chr15:83611658..83613627,2	MCF-7	breast:
2	chr15:83548573..83551400-chr15:83560401..83562858,2	MCF-7	breast:
3	chr15:83558288..83561120-chr15:83563049..83565497,2	MCF-7	breast:
4	chr15:83546371..83548475-chr15:83560322..83562996,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1021022	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12385947	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1256424	0.94[ASW][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1256426	0.89[YRI][hapmap]
rs1256428	0.84[JPT][hapmap]
rs1256436	0.85[ASN][1000 genomes]
rs1256438	0.95[ASN][1000 genomes]
rs1256439	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1256440	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1256441	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1256442	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1256443	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1256444	0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs1256445	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1256446	0.88[ASW][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1256447	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1256448	0.94[ASN][1000 genomes]
rs1256449	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1256450	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1256454	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17294229	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2621226	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2667377	0.94[ASW][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.94[YRI][hapmap]
rs2667378	0.81[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2667379	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2667380	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2667384	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3784377	0.85[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs55633961	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6603035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173264	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7173683	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs750234	0.82[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap]
rs8031927	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8036957	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs880289	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs899746	0.85[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][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	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2251275	RASGRF1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83520000-83563800	Weak transcription	Brain Hippocampus Middle	brain
2	chr15:83524600-83567800	Weak transcription	Left Ventricle	heart
3	chr15:83524800-83563800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr15:83540600-83573200	Weak transcription	Right Atrium	heart
5	chr15:83540800-83563600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:83541000-83566200	Weak transcription	Spleen	Spleen
7	chr15:83542400-83564000	Weak transcription	Lung	lung
8	chr15:83542400-83567200	Weak transcription	Brain Angular Gyrus	brain
9	chr15:83543600-83567600	Weak transcription	Aorta	Aorta
10	chr15:83544000-83563800	Weak transcription	Brain Anterior Caudate	brain
11	chr15:83544200-83560800	Weak transcription	Primary T cells from cord blood	blood
12	chr15:83554400-83564000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:83556000-83563800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr15:83556800-83563800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:83557400-83563800	Weak transcription	Brain Substantia Nigra	brain
16	chr15:83557600-83560600	Genic enhancers	Pancreas	Pancrea
17	chr15:83557800-83561400	Strong transcription	Liver	Liver
18	chr15:83558000-83563800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:83558200-83563800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:83558200-83563800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr15:83558200-83563800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:83558200-83564000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:83558200-83565000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:83558400-83563600	Weak transcription	HSMM	muscle
25	chr15:83558400-83569600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:83558600-83561600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:83558600-83563600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:83558600-83566600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:83558600-83567800	Weak transcription	Psoas Muscle	Psoas
30	chr15:83558800-83560600	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr15:83558800-83562000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:83559200-83563800	Weak transcription	Fetal Stomach	stomach
33	chr15:83559400-83561000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:83559600-83563800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr15:83559600-83570200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:83560000-83560600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr15:83560000-83560600	Enhancers	Gastric	stomach
38	chr15:83560000-83563600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr15:83560000-83563800	Weak transcription	Colon Smooth Muscle	Colon
40	chr15:83560200-83563800	Weak transcription	Fetal Muscle Leg	muscle
41	chr15:83560400-83563800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr15:83560400-83564200	Weak transcription	HSMMtube	muscle
43	chr15:83560400-83570200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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