Variant report

Variant	rs1256453
Chromosome Location	chr15:83543848-83543849
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83416895..83419331-chr15:83542514..83545188,2	K562	blood:
2	chr15:83543732..83546327-chr15:83548068..83551024,3	K562	blood:
3	chr15:83540274..83544098-chr15:83544468..83546572,4	K562	blood:

Variant related genes	Relation type
ENSG00000250988	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10906985	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11259959	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12385964	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1256429	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs1256434	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1256452	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1256455	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12905235	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs13380133	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553883	0.86[JPT][hapmap]
rs17360083	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2379992	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs2621227	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2621228	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2667382	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2667383	0.99[ASN][1000 genomes]
rs2667385	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41310978	0.94[ASN][1000 genomes]
rs4238539	0.88[JPT][hapmap]
rs62011731	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62011732	0.96[ASN][1000 genomes]
rs62011734	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7168760	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7169401	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8038679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9806543	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1256453	HOMER2	cis	Skin Sun Exposed Lower leg	GTEx
rs1256453	WHAMM	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83504600-83549400	Weak transcription	Psoas Muscle	Psoas
2	chr15:83519800-83544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:83520000-83549800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:83520000-83563800	Weak transcription	Brain Hippocampus Middle	brain
5	chr15:83520200-83547000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:83523600-83558000	Weak transcription	Esophagus	oesophagus
7	chr15:83524600-83567800	Weak transcription	Left Ventricle	heart
8	chr15:83524800-83563800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:83528000-83544000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:83537000-83551400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:83538000-83549600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:83540000-83544000	Weak transcription	Osteobl	bone
13	chr15:83540000-83544200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:83540200-83544000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:83540200-83544200	Weak transcription	Fetal Intestine Small	intestine
16	chr15:83540200-83545400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr15:83540400-83544600	Weak transcription	HepG2	liver
18	chr15:83540600-83573200	Weak transcription	Right Atrium	heart
19	chr15:83540800-83544000	Strong transcription	Stomach Smooth Muscle	stomach
20	chr15:83540800-83563600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:83541000-83566200	Weak transcription	Spleen	Spleen
22	chr15:83541200-83545600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:83541400-83544200	Strong transcription	Liver	Liver
24	chr15:83541600-83544200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr15:83541600-83545000	Weak transcription	Colon Smooth Muscle	Colon
26	chr15:83541800-83544000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:83541800-83544000	Strong transcription	Gastric	stomach
28	chr15:83542200-83544400	Strong transcription	Fetal Muscle Leg	muscle
29	chr15:83542200-83544600	Weak transcription	Fetal Brain Female	brain
30	chr15:83542400-83544000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:83542400-83544000	Weak transcription	HSMMtube	muscle
32	chr15:83542400-83551000	Weak transcription	Right Ventricle	heart
33	chr15:83542400-83564000	Weak transcription	Lung	lung
34	chr15:83542400-83567200	Weak transcription	Brain Angular Gyrus	brain
35	chr15:83542800-83544200	Strong transcription	Primary T cells from cord blood	blood
36	chr15:83542800-83558000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:83543000-83544200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:83543000-83544200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
39	chr15:83543000-83557600	Weak transcription	Fetal Stomach	stomach
40	chr15:83543200-83544200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:83543400-83544000	Strong transcription	Brain Anterior Caudate	brain
42	chr15:83543400-83545000	Genic enhancers	Pancreas	Pancrea
43	chr15:83543400-83545200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:83543600-83545000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:83543600-83545000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr15:83543600-83545000	Enhancers	HSMM	muscle
47	chr15:83543600-83557800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:83543600-83558000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:83543600-83567600	Weak transcription	Aorta	Aorta
50	chr15:83543800-83544000	Strong transcription	Fetal Muscle Trunk	muscle

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