Variant report

Variant	rs1256425
Chromosome Location	chr15:83523956-83523957
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	chr15:83522860..83525020-chr15:83654105..83656593,2	MCF-7	breast:
2	chr15:83518647..83521952-chr15:83521961..83525177,3	K562	blood:

Variant related genes	Relation type
ENSG00000169612	Chromatin interaction
ENSG00000103942	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12385964	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1256429	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1256451	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1256455	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1256456	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12905235	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2458017	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2667383	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2928572	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41310978	0.83[EUR][1000 genomes]
rs62011732	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8038679	0.90[AMR][1000 genomes];0.86[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1256425	WHAMM	cis	Adipose Subcutaneous	GTEx
rs1256425	RPS17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83504600-83549400	Weak transcription	Psoas Muscle	Psoas
2	chr15:83506000-83524200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:83506200-83527400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:83506200-83543800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:83507200-83539400	Weak transcription	Fetal Intestine Small	intestine
6	chr15:83513200-83532000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:83514400-83542800	Weak transcription	Primary T cells from cord blood	blood
8	chr15:83518800-83524200	Weak transcription	Lung	lung
9	chr15:83519000-83524200	Weak transcription	Left Ventricle	heart
10	chr15:83519000-83524400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:83519000-83524600	Weak transcription	Adipose Nuclei	Adipose
12	chr15:83519000-83524800	Weak transcription	Right Atrium	heart
13	chr15:83519000-83535800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:83519000-83541400	Weak transcription	Brain Anterior Caudate	brain
15	chr15:83519200-83524200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:83519200-83524200	Weak transcription	Right Ventricle	heart
17	chr15:83519200-83524400	Strong transcription	Gastric	stomach
18	chr15:83519200-83528800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:83519200-83536200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:83519400-83525800	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:83519600-83524200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:83519600-83524200	Weak transcription	HepG2	liver
23	chr15:83519600-83524200	Weak transcription	K562	blood
24	chr15:83519600-83525600	Weak transcription	HSMMtube	muscle
25	chr15:83519600-83529600	Weak transcription	Brain Substantia Nigra	brain
26	chr15:83519800-83544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:83520000-83524400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:83520000-83543600	Weak transcription	HSMM	muscle
29	chr15:83520000-83549800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:83520000-83563800	Weak transcription	Brain Hippocampus Middle	brain
31	chr15:83520200-83542000	Weak transcription	Brain Angular Gyrus	brain
32	chr15:83520200-83547000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:83521000-83524200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:83521000-83524400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr15:83521600-83524600	Weak transcription	Osteobl	bone
36	chr15:83521800-83524200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr15:83521800-83526400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr15:83521800-83529400	Weak transcription	Primary B cells from cord blood	blood
39	chr15:83522000-83524200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr15:83522000-83524400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:83522200-83524400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr15:83522200-83524400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr15:83522400-83524000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:83522400-83524200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:83522400-83524600	Weak transcription	NH-A	brain
46	chr15:83522400-83543400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr15:83522600-83524000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:83522600-83529000	Weak transcription	Fetal Kidney	kidney
49	chr15:83522600-83542200	Weak transcription	Fetal Muscle Leg	muscle
50	chr15:83522800-83524000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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