Variant report

Variant	rs1256429
Chromosome Location	chr15:83521036-83521037
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr15:83520748-83521269	SK-N-SH	brain:	n/a	n/a
2	CEBPB	chr15:83520711-83521225	IMR90	lung:	n/a	n/a
3	RCOR1	chr15:83520572-83521430	IMR90	lung:	n/a	n/a
4	PBX3	chr15:83520587-83521287	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:83517113..83521654-chr15:83652714..83657006,7	MCF-7	breast:
2	chr15:83519425..83521228-chr15:83661730..83663571,2	K562	blood:

Variant related genes	Relation type
HOMER2	TF binding region
ENSG00000169612	Chromatin interaction
ENSG00000103942	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1105867	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs12385964	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1256425	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1256434	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1256451	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1256452	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs1256453	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs1256455	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]
rs1256456	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12905235	0.89[CEU][hapmap];0.92[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12914161	0.84[EUR][1000 genomes]
rs1553883	0.89[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs17360083	0.82[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs1877241	0.94[CEU][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs2089844	0.81[EUR][1000 genomes]
rs2379992	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2379993	0.84[EUR][1000 genomes]
rs2458017	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2621227	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs2621228	0.92[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs2667383	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2667385	0.92[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs2890313	0.94[CEU][hapmap]
rs2928572	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41310978	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4238539	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62011732	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7163402	1.00[CEU][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7169401	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs8038679	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9806543	0.92[CHB][hapmap];0.90[CHD][hapmap];0.86[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1256429	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs1256429	RASGRF1	cis	cerebellum	SCAN
rs1256429	BTBD1	cis	parietal	SCAN
rs1256429	WHAMM	cis	cerebellum	SCAN
rs1256429	BTBD1	cis	cerebellum	SCAN
rs1256429	RASGRF1	cis	parietal	SCAN
rs1256429	WHAMM	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:79 , 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	chr15:83507800-83521800	Weak transcription	Brain Germinal Matrix	brain
8	chr15:83513200-83532000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:83514200-83521600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr15:83514400-83542800	Weak transcription	Primary T cells from cord blood	blood
11	chr15:83516000-83523400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:83517800-83522800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr15:83518200-83522600	Enhancers	Fetal Brain Female	brain
14	chr15:83518200-83523000	Enhancers	Fetal Thymus	thymus
15	chr15:83518400-83522800	Enhancers	Fetal Brain Male	brain
16	chr15:83518600-83522400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:83518800-83524200	Weak transcription	Lung	lung
18	chr15:83519000-83521200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr15:83519000-83521200	Weak transcription	Osteobl	bone
20	chr15:83519000-83521800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr15:83519000-83523400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:83519000-83524200	Weak transcription	Left Ventricle	heart
23	chr15:83519000-83524400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:83519000-83524600	Weak transcription	Adipose Nuclei	Adipose
25	chr15:83519000-83524800	Weak transcription	Right Atrium	heart
26	chr15:83519000-83535800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:83519000-83541400	Weak transcription	Brain Anterior Caudate	brain
28	chr15:83519200-83521200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:83519200-83521400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr15:83519200-83521800	Strong transcription	Liver	Liver
31	chr15:83519200-83522000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr15:83519200-83523400	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:83519200-83524200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr15:83519200-83524200	Weak transcription	Right Ventricle	heart
35	chr15:83519200-83524400	Strong transcription	Gastric	stomach
36	chr15:83519200-83528800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr15:83519200-83536200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:83519400-83521400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr15:83519400-83521600	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:83519400-83525800	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:83519600-83521800	Genic enhancers	Fetal Muscle Leg	muscle
42	chr15:83519600-83522000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:83519600-83523400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:83519600-83523600	Strong transcription	Esophagus	oesophagus
45	chr15:83519600-83524200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:83519600-83524200	Weak transcription	HepG2	liver
47	chr15:83519600-83524200	Weak transcription	K562	blood
48	chr15:83519600-83525600	Weak transcription	HSMMtube	muscle
49	chr15:83519600-83529600	Weak transcription	Brain Substantia Nigra	brain
50	chr15:83519800-83521800	Strong transcription	Pancreas	Pancrea

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