Variant report

Variant	rs1256428
Chromosome Location	chr15:83521818-83521819
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:83521559..83523474-chr15:83548872..83551411,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1256424	0.85[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1256436	0.82[AFR][1000 genomes]
rs1256438	0.80[AFR][1000 genomes]
rs1256439	0.94[ASW][hapmap];0.81[CEU][hapmap];0.84[JPT][hapmap];0.80[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap]
rs1256444	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]
rs1256446	0.81[CEU][hapmap];0.89[JPT][hapmap]
rs1256447	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs1256449	0.89[CEU][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap]
rs1256454	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs17294229	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs2251275	0.84[JPT][hapmap]
rs2621226	0.81[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap]
rs2667377	0.81[CEU][hapmap]
rs2667378	0.81[CEU][hapmap]
rs2667379	0.85[CEU][hapmap]
rs2667384	0.84[JPT][hapmap]
rs6603035	0.84[JPT][hapmap]
rs750234	0.85[GIH][hapmap];0.84[JPT][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1256428	EFTUD1	cis	parietal	SCAN
rs1256428	RASGRF1	cis	cerebellum	SCAN
rs1256428	WHAMM	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83504600-83549400	Weak transcription	Psoas Muscle	Psoas
2	chr15:83505800-83522400	Weak transcription	Fetal Kidney	kidney
3	chr15:83506000-83524200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:83506200-83527400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:83506200-83543800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:83507200-83539400	Weak transcription	Fetal Intestine Small	intestine
7	chr15:83513200-83532000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:83514400-83542800	Weak transcription	Primary T cells from cord blood	blood
9	chr15:83516000-83523400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:83517800-83522800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr15:83518200-83522600	Enhancers	Fetal Brain Female	brain
12	chr15:83518200-83523000	Enhancers	Fetal Thymus	thymus
13	chr15:83518400-83522800	Enhancers	Fetal Brain Male	brain
14	chr15:83518600-83522400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:83518800-83524200	Weak transcription	Lung	lung
16	chr15:83519000-83523400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:83519000-83524200	Weak transcription	Left Ventricle	heart
18	chr15:83519000-83524400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:83519000-83524600	Weak transcription	Adipose Nuclei	Adipose
20	chr15:83519000-83524800	Weak transcription	Right Atrium	heart
21	chr15:83519000-83535800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr15:83519000-83541400	Weak transcription	Brain Anterior Caudate	brain
23	chr15:83519200-83522000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr15:83519200-83523400	Weak transcription	Colon Smooth Muscle	Colon
25	chr15:83519200-83524200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:83519200-83524200	Weak transcription	Right Ventricle	heart
27	chr15:83519200-83524400	Strong transcription	Gastric	stomach
28	chr15:83519200-83528800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr15:83519200-83536200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:83519400-83525800	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:83519600-83522000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:83519600-83523400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr15:83519600-83523600	Strong transcription	Esophagus	oesophagus
34	chr15:83519600-83524200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:83519600-83524200	Weak transcription	HepG2	liver
36	chr15:83519600-83524200	Weak transcription	K562	blood
37	chr15:83519600-83525600	Weak transcription	HSMMtube	muscle
38	chr15:83519600-83529600	Weak transcription	Brain Substantia Nigra	brain
39	chr15:83519800-83523800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:83519800-83544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:83520000-83524400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:83520000-83543600	Weak transcription	HSMM	muscle
43	chr15:83520000-83549800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr15:83520000-83563800	Weak transcription	Brain Hippocampus Middle	brain
45	chr15:83520200-83522200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:83520200-83542000	Weak transcription	Brain Angular Gyrus	brain
47	chr15:83520200-83547000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:83520400-83523400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:83520600-83522000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:83520600-83522400	Enhancers	NH-A	brain

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