Variant report

Variant	rs1256455
Chromosome Location	chr15:83544522-83544523
allele	C/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: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10906985	0.99[ASN][1000 genomes]
rs1105867	0.89[CEU][hapmap]
rs11259959	0.94[ASN][1000 genomes]
rs12385964	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1256425	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1256429	0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1256434	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1256451	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256452	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1256453	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1256456	0.84[EUR][1000 genomes]
rs12905235	0.84[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.85[EUR][1000 genomes]
rs13380133	0.97[ASN][1000 genomes]
rs1553883	0.84[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap]
rs1553885	1.00[LWK][hapmap]
rs17360083	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1877241	1.00[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs2379992	0.86[JPT][hapmap]
rs2379993	0.80[EUR][1000 genomes]
rs2458017	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2621227	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2621228	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2667382	0.92[ASN][1000 genomes]
rs2667383	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2667385	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2890313	1.00[CEU][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap]
rs2928572	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs41310978	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238539	0.94[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs62011731	0.94[ASN][1000 genomes]
rs62011732	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62011734	0.99[ASN][1000 genomes]
rs7163402	0.94[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs7168760	0.94[ASN][1000 genomes]
rs7169401	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8038679	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9806543	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1256455	BTBD1	cis	parietal	SCAN
rs1256455	RASGRF1	cis	cerebellum	SCAN
rs1256455	EFTUD1	cis	cerebellum	SCAN
rs1256455	PACS2	trans	cerebellum	SCAN
rs1256455	BTBD1	cis	cerebellum	SCAN
rs1256455	WHAMM	cis	cerebellum	SCAN
rs1256455	WHAMM	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83504600-83549400	Weak transcription	Psoas Muscle	Psoas
2	chr15:83520000-83549800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:83520000-83563800	Weak transcription	Brain Hippocampus Middle	brain
4	chr15:83520200-83547000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:83523600-83558000	Weak transcription	Esophagus	oesophagus
6	chr15:83524600-83567800	Weak transcription	Left Ventricle	heart
7	chr15:83524800-83563800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr15:83537000-83551400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:83538000-83549600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:83540200-83545400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:83540400-83544600	Weak transcription	HepG2	liver
12	chr15:83540600-83573200	Weak transcription	Right Atrium	heart
13	chr15:83540800-83563600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:83541000-83566200	Weak transcription	Spleen	Spleen
15	chr15:83541200-83545600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:83541600-83545000	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:83542200-83544600	Weak transcription	Fetal Brain Female	brain
18	chr15:83542400-83551000	Weak transcription	Right Ventricle	heart
19	chr15:83542400-83564000	Weak transcription	Lung	lung
20	chr15:83542400-83567200	Weak transcription	Brain Angular Gyrus	brain
21	chr15:83542800-83558000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:83543000-83557600	Weak transcription	Fetal Stomach	stomach
23	chr15:83543400-83545000	Genic enhancers	Pancreas	Pancrea
24	chr15:83543400-83545200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:83543600-83545000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:83543600-83545000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr15:83543600-83545000	Enhancers	HSMM	muscle
28	chr15:83543600-83557800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:83543600-83558000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:83543600-83567600	Weak transcription	Aorta	Aorta
31	chr15:83543800-83544800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr15:83543800-83544800	Enhancers	NHDF-Ad	bronchial
33	chr15:83544000-83544600	Enhancers	HSMMtube	muscle
34	chr15:83544000-83544800	Enhancers	NHEK	skin
35	chr15:83544000-83545000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:83544000-83545000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:83544000-83545000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:83544000-83545000	Enhancers	HMEC	breast
39	chr15:83544000-83545000	Enhancers	NH-A	brain
40	chr15:83544000-83545000	Enhancers	Osteobl	bone
41	chr15:83544000-83550800	Weak transcription	Gastric	stomach
42	chr15:83544000-83551000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr15:83544000-83558000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:83544000-83558000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr15:83544000-83563800	Weak transcription	Brain Anterior Caudate	brain
46	chr15:83544200-83544800	Enhancers	NHLF	lung
47	chr15:83544200-83545000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:83544200-83545000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr15:83544200-83546400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr15:83544200-83549000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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