Variant report

Variant	rs1256447
Chromosome Location	chr15:83542167-83542168
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:83540274..83544098-chr15:83544468..83546572,4	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1021022	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12385947	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1256424	0.96[CEU][hapmap];0.81[GIH][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1256428	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs1256436	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1256438	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256439	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256440	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256441	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256442	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256443	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256444	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256445	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256446	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256448	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256449	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256450	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256454	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17294229	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2251275	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]
rs2621226	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2667377	1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap]
rs2667378	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2667379	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2667380	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2667384	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3784377	0.83[MKK][hapmap]
rs55633961	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6603035	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7173264	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7173683	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs750234	0.89[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap]
rs8031927	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8036957	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs880289	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs899746	0.83[MKK][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1256447	RASGRF1	cis	parietal	SCAN
rs1256447	RASGRF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83504600-83549400	Weak transcription	Psoas Muscle	Psoas
2	chr15:83506200-83543800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:83514400-83542800	Weak transcription	Primary T cells from cord blood	blood
4	chr15:83519800-83544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:83520000-83543600	Weak transcription	HSMM	muscle
6	chr15:83520000-83549800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr15:83520000-83563800	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:83520200-83547000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:83522400-83543400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr15:83522600-83542200	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:83523600-83558000	Weak transcription	Esophagus	oesophagus
12	chr15:83524600-83567800	Weak transcription	Left Ventricle	heart
13	chr15:83524800-83563800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:83528000-83544000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:83537000-83551400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:83538000-83549600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:83540000-83543000	Weak transcription	Fetal Intestine Large	intestine
18	chr15:83540000-83544000	Weak transcription	Osteobl	bone
19	chr15:83540000-83544200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:83540200-83544000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:83540200-83544200	Weak transcription	Fetal Intestine Small	intestine
22	chr15:83540200-83545400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:83540400-83543000	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr15:83540400-83544600	Weak transcription	HepG2	liver
25	chr15:83540600-83573200	Weak transcription	Right Atrium	heart
26	chr15:83540800-83544000	Strong transcription	Stomach Smooth Muscle	stomach
27	chr15:83540800-83563600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:83541000-83542400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:83541000-83566200	Weak transcription	Spleen	Spleen
30	chr15:83541200-83542200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:83541200-83545600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:83541400-83542400	Enhancers	Right Ventricle	heart
33	chr15:83541400-83543000	Strong transcription	Brain Anterior Caudate	brain
34	chr15:83541400-83543000	Strong transcription	Fetal Stomach	stomach
35	chr15:83541400-83543200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:83541400-83544200	Strong transcription	Liver	Liver
37	chr15:83541600-83542800	Enhancers	Fetal Heart	heart
38	chr15:83541600-83543600	Strong transcription	Aorta	Aorta
39	chr15:83541600-83544200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr15:83541600-83545000	Weak transcription	Colon Smooth Muscle	Colon
41	chr15:83541800-83542400	Strong transcription	HSMMtube	muscle
42	chr15:83541800-83544000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr15:83541800-83544000	Strong transcription	Gastric	stomach
44	chr15:83542000-83542400	Strong transcription	Brain Angular Gyrus	brain
45	chr15:83542000-83542400	ZNF genes & repeats	Lung	lung
46	chr15:83542000-83542800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:83542000-83542800	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr15:83542000-83543200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:83542000-83543400	Strong transcription	Pancreas	Pancrea
50	chr15:83542000-83543600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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