Variant report

Variant	rs2590480
Chromosome Location	chr14:81224326-81224327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10136404	0.84[CHD][hapmap];0.91[MEX][hapmap]
rs1016507	0.88[CHB][hapmap];1.00[YRI][hapmap]
rs1025253	0.94[CHD][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs12431821	0.91[ASW][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap]
rs12878945	0.83[CHD][hapmap]
rs12880014	0.96[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12888082	1.00[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs12891585	0.92[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12892825	0.85[CHD][hapmap]
rs12896065	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1458993	0.88[CHB][hapmap]
rs1597320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17111270	0.80[TSI][hapmap]
rs17542615	0.87[CHB][hapmap];0.85[YRI][hapmap]
rs17542712	0.83[CHD][hapmap]
rs17613911	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17614081	0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs1992973	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2217176	0.94[CHD][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs2246617	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs228120	1.00[YRI][hapmap]
rs2371413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2371416	0.82[CHB][hapmap]
rs2371457	1.00[YRI][hapmap]
rs2371462	0.82[MEX][hapmap]
rs2596118	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34848301	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742721	0.85[CHD][hapmap]
rs3742722	0.85[CHD][hapmap]
rs4523859	1.00[ASW][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs4903948	0.81[ASW][hapmap];0.94[CHD][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs6574605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6574613	0.91[CHD][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs7141434	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7145233	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7148368	0.91[CHD][hapmap];0.82[MEX][hapmap]
rs7148618	0.87[CHB][hapmap];1.00[YRI][hapmap]
rs7150858	0.91[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap]
rs7153979	0.97[CHD][hapmap];0.85[TSI][hapmap]
rs7154132	0.81[ASW][hapmap];0.94[CHD][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs759916	0.81[ASW][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs8005809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8006864	1.00[YRI][hapmap]
rs8016601	1.00[YRI][hapmap]
rs8017943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8021137	1.00[YRI][hapmap]
rs8022411	1.00[YRI][hapmap]
rs8023233	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv869348	chr14:80921098-81535754	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv565290	chr14:81085129-81230117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1035295	chr14:81180999-81236636	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2590480	C14orf145	cis	parietal	SCAN
rs2590480	VIPAR	cis	parietal	SCAN
rs2590480	C14orf145	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:81182800-81224600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr14:81192800-81305400	Weak transcription	Primary B cells from cord blood	blood
3	chr14:81199800-81248600	Weak transcription	Primary T cells from cord blood	blood
4	chr14:81203800-81229000	Weak transcription	Left Ventricle	heart
5	chr14:81205000-81261000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr14:81206400-81226800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr14:81207200-81232600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr14:81207600-81226200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr14:81207600-81230800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr14:81207600-81265400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr14:81208400-81240400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr14:81208800-81232400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr14:81209400-81227800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr14:81209400-81229000	Weak transcription	Fetal Lung	lung
15	chr14:81209600-81248200	Weak transcription	HSMM	muscle
16	chr14:81210600-81230400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr14:81212800-81227000	Weak transcription	Adipose Nuclei	Adipose
18	chr14:81213400-81231200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr14:81215800-81236200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr14:81219200-81228600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr14:81220200-81224800	Strong transcription	Fetal Thymus	thymus
22	chr14:81220600-81227000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr14:81220600-81229200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr14:81221000-81238600	Weak transcription	Ovary	ovary
25	chr14:81221200-81230800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr14:81221400-81238600	Weak transcription	Thymus	Thymus
27	chr14:81221600-81236200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr14:81221800-81229000	Weak transcription	NHDF-Ad	bronchial
29	chr14:81222400-81260000	Weak transcription	Fetal Brain Female	brain
30	chr14:81223000-81230800	Weak transcription	NHEK	skin
31	chr14:81223200-81229000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr14:81223200-81250800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr14:81223400-81234000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr14:81224000-81224800	Weak transcription	Dnd41	blood

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