Variant report

Variant	rs1256444
Chromosome Location	chr15:83540253-83540254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:83517714..83519643-chr15:83539190..83541099,2	MCF-7	breast:
2	chr15:83539080..83540967-chr15:83679708..83682036,2	K562	blood:

Variant related genes	Relation type
ENSG00000260608	Chromatin interaction
ENSG00000103942	Chromatin interaction
ENSG00000169609	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1021022	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12385947	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256424	0.89[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs1256428	0.94[ASW][hapmap];0.89[CEU][hapmap];0.82[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs1256436	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1256438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256439	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256440	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256441	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256442	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256443	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256445	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256446	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256447	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]
rs1256448	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256450	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256454	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17294229	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2251275	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]
rs2621226	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2667377	0.92[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap]
rs2667378	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs2667379	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs2667380	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2667384	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55633961	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6603035	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7173264	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173683	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs750234	0.82[CEU][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs8031927	0.96[ASN][1000 genomes]
rs8036957	0.96[ASN][1000 genomes]
rs880289	0.93[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1256444	EFTUD1	cis	parietal	SCAN
rs1256444	RASGRF1	cis	cerebellum	SCAN
rs1256444	RASGRF1	cis	parietal	SCAN

Chromatin state (count:48 , 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	chr15:83519000-83541400	Weak transcription	Brain Anterior Caudate	brain
5	chr15:83519800-83544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:83520000-83543600	Weak transcription	HSMM	muscle
7	chr15:83520000-83549800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:83520000-83563800	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:83520200-83542000	Weak transcription	Brain Angular Gyrus	brain
10	chr15:83520200-83547000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:83522400-83543400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:83522600-83542200	Weak transcription	Fetal Muscle Leg	muscle
13	chr15:83523400-83540800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:83523600-83541400	Weak transcription	Fetal Stomach	stomach
15	chr15:83523600-83558000	Weak transcription	Esophagus	oesophagus
16	chr15:83524600-83567800	Weak transcription	Left Ventricle	heart
17	chr15:83524800-83563800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr15:83526000-83541800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:83528000-83540400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr15:83528000-83540800	Weak transcription	Gastric	stomach
21	chr15:83528000-83542000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:83528000-83544000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:83537000-83551400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:83537400-83540400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:83538000-83549600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:83539000-83541000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr15:83539000-83541000	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr15:83539000-83541800	Enhancers	Primary hematopoietic stem cells	blood
29	chr15:83539000-83542000	Genic enhancers	Pancreas	Pancrea
30	chr15:83539200-83541600	Enhancers	Primary B cells from peripheral blood	blood
31	chr15:83539200-83542000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:83539400-83540600	Enhancers	Duodenum Mucosa	Duodenum
33	chr15:83539400-83541200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:83539400-83541600	Enhancers	Primary B cells from cord blood	blood
35	chr15:83539600-83540400	Enhancers	HSMMtube	muscle
36	chr15:83539600-83541000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:83539800-83540600	Enhancers	Liver	Liver
38	chr15:83540000-83540400	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr15:83540000-83540400	Enhancers	HepG2	liver
40	chr15:83540000-83540400	Bivalent Enhancer	K562	blood
41	chr15:83540000-83543000	Weak transcription	Fetal Intestine Large	intestine
42	chr15:83540000-83544000	Weak transcription	Osteobl	bone
43	chr15:83540000-83544200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr15:83540200-83540400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:83540200-83540600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:83540200-83544000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:83540200-83544200	Weak transcription	Fetal Intestine Small	intestine
48	chr15:83540200-83545400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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