Variant report

Variant	rs1045004
Chromosome Location	chr14:55819791-55819792
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:55727647..55729391-chr14:55818839..55821445,2	MCF-7	breast:
2	chr14:55813775..55816746-chr14:55819381..55821287,2	MCF-7	breast:
3	chr14:55812369..55814760-chr14:55818097..55821866,3	MCF-7	breast:
4	chr14:55817121..55819281-chr14:55819678..55821286,2	MCF-7	breast:
5	chr14:55736450..55738716-chr14:55817481..55820238,2	K562	blood:
6	chr14:55736773..55740408-chr14:55819454..55822170,5	MCF-7	breast:
7	chr14:55809381..55811401-chr14:55819564..55823074,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178974	Chromatin interaction
ENSG00000258413	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10129505	0.95[JPT][hapmap];0.85[YRI][hapmap]
rs10131562	0.94[JPT][hapmap]
rs10131730	0.95[JPT][hapmap];0.85[YRI][hapmap]
rs10134213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10134317	0.89[ASW][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs10134339	0.81[JPT][hapmap]
rs10136596	0.90[JPT][hapmap]
rs10137307	0.90[JPT][hapmap]
rs10140869	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs10141396	1.00[ASW][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10141552	0.95[JPT][hapmap]
rs10142448	0.95[JPT][hapmap]
rs10144418	1.00[ASW][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs10146637	0.95[JPT][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap];0.81[YRI][hapmap]
rs10150760	0.95[JPT][hapmap]
rs1045002	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs1109170	0.81[JPT][hapmap]
rs11158034	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs11621265	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11625001	0.95[JPT][hapmap]
rs11626485	0.96[EUR][1000 genomes]
rs11628437	0.95[JPT][hapmap]
rs11851169	0.95[JPT][hapmap]
rs11851870	0.85[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs1572611	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs17674463	0.95[JPT][hapmap]
rs17674563	0.90[AFR][1000 genomes]
rs17740741	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs17741542	0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap]
rs17741831	0.95[JPT][hapmap]
rs17742719	0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs1972221	0.95[JPT][hapmap];0.85[YRI][hapmap]
rs2009291	0.80[JPT][hapmap]
rs2026633	1.00[ASW][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs2039039	0.90[EUR][1000 genomes]
rs2209808	0.86[AFR][1000 genomes]
rs2880103	0.90[JPT][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap];0.81[YRI][hapmap]
rs3742569	0.95[JPT][hapmap]
rs3783650	0.81[JPT][hapmap]
rs3783651	0.89[JPT][hapmap]
rs3783652	0.95[JPT][hapmap]
rs3825616	0.81[JPT][hapmap]
rs4597235	0.85[JPT][hapmap]
rs58296156	0.94[AFR][1000 genomes]
rs60726667	0.83[EUR][1000 genomes]
rs6573017	0.81[JPT][hapmap]
rs7144737	0.95[JPT][hapmap]
rs7147136	0.90[AFR][1000 genomes]
rs7147247	0.95[JPT][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap];0.85[YRI][hapmap]
rs7150234	0.83[AFR][1000 genomes]
rs7150763	0.95[JPT][hapmap]
rs7151581	0.89[ASW][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs7152390	0.94[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs7153110	0.81[JPT][hapmap]
rs7154831	0.94[AFR][1000 genomes]
rs7154889	0.81[JPT][hapmap]
rs7155954	0.94[JPT][hapmap]
rs7158768	0.81[JPT][hapmap]
rs7158791	0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs7159144	0.81[JPT][hapmap]
rs7159824	0.95[JPT][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap];0.85[YRI][hapmap]
rs8005450	0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs8006525	0.81[JPT][hapmap]
rs8013713	0.95[JPT][hapmap]
rs8014477	0.86[ASW][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap]
rs8014540	0.95[JPT][hapmap];0.85[YRI][hapmap]
rs8015211	0.87[ASW][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap]
rs8021583	0.95[JPT][hapmap]
rs8023197	0.81[JPT][hapmap]
rs9323285	0.90[JPT][hapmap];0.91[LWK][hapmap];0.81[YRI][hapmap]
rs946059	0.81[JPT][hapmap]
rs9919923	0.94[AFR][1000 genomes]
rs9919926	0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs9919932	0.95[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039438	chr14:55746585-55886099	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv901957	chr14:55819219-55853724	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1045004	FBXO34	cis	cerebellum	SCAN
rs1045004	TRIM9	cis	parietal	SCAN
rs1045004	C14orf37	cis	parietal	SCAN
rs1045004	FBXO34	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55800600-55823600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr14:55801200-55842800	Weak transcription	Fetal Brain Male	brain
3	chr14:55806800-55820800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr14:55808800-55865200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr14:55811200-55820600	Weak transcription	Fetal Heart	heart
6	chr14:55813600-55837200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr14:55814000-55830400	Weak transcription	Colon Smooth Muscle	Colon
8	chr14:55814400-55853200	Weak transcription	Right Atrium	heart
9	chr14:55815400-55820600	Weak transcription	Psoas Muscle	Psoas
10	chr14:55816000-55837200	Weak transcription	K562	blood
11	chr14:55816200-55820600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr14:55816400-55823600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr14:55816600-55823000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr14:55817000-55819800	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr14:55817000-55819800	Strong transcription	Thymus	Thymus
16	chr14:55817000-55820000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr14:55817000-55820000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr14:55817000-55820000	Strong transcription	Osteobl	bone
19	chr14:55817000-55820200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr14:55817000-55821000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr14:55817000-55822800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr14:55817200-55819800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr14:55817200-55819800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr14:55817200-55819800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr14:55817200-55819800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr14:55817200-55819800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr14:55817200-55819800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr14:55817200-55819800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr14:55817200-55819800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr14:55817200-55819800	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr14:55817200-55819800	Strong transcription	Fetal Brain Female	brain
32	chr14:55817200-55819800	Strong transcription	Fetal Muscle Leg	muscle
33	chr14:55817200-55819800	Strong transcription	Placenta	Placenta
34	chr14:55817200-55819800	Strong transcription	Fetal Thymus	thymus
35	chr14:55817200-55819800	Strong transcription	Left Ventricle	heart
36	chr14:55817200-55819800	Strong transcription	HSMM	muscle
37	chr14:55817200-55820000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr14:55817200-55820000	Strong transcription	Liver	Liver
39	chr14:55817200-55820000	Strong transcription	Duodenum Mucosa	Duodenum
40	chr14:55817200-55820000	Strong transcription	HMEC	breast
41	chr14:55817200-55820000	Strong transcription	NHDF-Ad	bronchial
42	chr14:55817200-55820200	Strong transcription	Fetal Intestine Large	intestine
43	chr14:55817200-55821000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr14:55817200-55822800	Strong transcription	GM12878-XiMat	blood
45	chr14:55817200-55823000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr14:55817200-55823200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr14:55817200-55823200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr14:55817200-55823800	Strong transcription	Dnd41	blood
49	chr14:55817200-55826200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr14:55817200-55826400	Strong transcription	Fetal Stomach	stomach

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