Variant report

Variant	rs4290414
Chromosome Location	chr14:81869491-81869492
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:81867720..81869556-chr14:81873808..81876587,2	MCF-7	breast:
2	chr14:81867994..81870092-chr14:81876125..81877918,2	K562	blood:
3	chr14:81816828..81818366-chr14:81868014..81870055,2	K562	blood:
4	chr14:81865587..81872038-chr14:81887440..81896764,13	K562	blood:
5	chr14:81684503..81687134-chr14:81866673..81870053,4	K562	blood:
6	chr14:81685583..81687332-chr14:81866862..81869553,2	K562	blood:

Variant related genes	Relation type
ENSG00000140022	Chromatin interaction
ENSG00000165417	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1003258	0.91[CHB][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10134500	0.82[AMR][1000 genomes]
rs10134510	0.95[MEX][hapmap];0.82[AMR][1000 genomes]
rs10135926	0.91[CHB][hapmap];0.80[GIH][hapmap];0.89[ASN][1000 genomes]
rs10146094	0.82[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes]
rs10146257	0.84[AMR][1000 genomes]
rs10147416	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10147793	1.00[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes]
rs11850462	0.82[AMR][1000 genomes]
rs12588572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569012	0.91[CHB][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17111790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111797	1.00[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes]
rs2145123	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2371596	0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2371599	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2371602	0.90[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs28476767	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3825606	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3844533	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3844534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3853419	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3853420	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3853421	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3915222	0.91[CHB][hapmap];0.85[LWK][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4110459	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4110460	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4110462	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4275784	0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4903982	0.90[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs6574649	0.81[ASN][1000 genomes]
rs6574650	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6574651	0.91[CHB][hapmap];0.85[LWK][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6574653	0.90[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs6574654	0.91[ASN][1000 genomes]
rs6574655	0.86[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.82[ASN][1000 genomes]
rs7145713	0.86[CHB][hapmap]
rs7153104	0.89[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7153556	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs7153600	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7156951	0.91[ASN][1000 genomes]
rs7160907	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs72703752	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72703760	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8014268	0.83[AMR][1000 genomes]
rs8018198	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8020806	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8022070	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9652383	0.91[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3358936	chr14:81786719-81928269	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
2	nsv902119	chr14:81810945-81884857	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1047694	chr14:81831147-82534026	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv542145	chr14:81831147-82534026	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4290414	SPTLC2	cis	cerebellum	SCAN
rs4290414	NGB	cis	cerebellum	SCAN
rs4290414	STON2	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:81836400-81885800	Weak transcription	Gastric	stomach
2	chr14:81852800-81899800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:81861000-81873000	Weak transcription	HepG2	liver
4	chr14:81861400-81889400	Weak transcription	Fetal Kidney	kidney
5	chr14:81861600-81873200	Weak transcription	Brain Hippocampus Middle	brain
6	chr14:81862800-81881400	Weak transcription	Fetal Intestine Small	intestine
7	chr14:81864400-81893600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr14:81864600-81870000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr14:81865000-81884600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr14:81865000-81885600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr14:81865000-81889400	Weak transcription	Ovary	ovary
12	chr14:81865000-81892400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr14:81865200-81870000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr14:81865400-81873000	Weak transcription	Liver	Liver
15	chr14:81867600-81892000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr14:81867800-81869800	Enhancers	HSMM	muscle
17	chr14:81867800-81870000	Enhancers	NHDF-Ad	bronchial
18	chr14:81867800-81870200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr14:81867800-81870200	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr14:81867800-81873000	Weak transcription	Fetal Muscle Leg	muscle
21	chr14:81867800-81889800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr14:81868200-81870000	Enhancers	Esophagus	oesophagus
23	chr14:81868400-81873000	Weak transcription	Adipose Nuclei	Adipose
24	chr14:81868400-81884000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr14:81868600-81874200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr14:81868800-81873000	Weak transcription	Brain Anterior Caudate	brain
27	chr14:81868800-81881600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr14:81868800-81893600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr14:81869000-81870000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr14:81869000-81873000	Weak transcription	Placenta	Placenta
31	chr14:81869200-81869800	Weak transcription	Spleen	Spleen
32	chr14:81869200-81870000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr14:81869200-81872200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr14:81869200-81872800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr14:81869200-81873000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr14:81869200-81873000	Weak transcription	Psoas Muscle	Psoas
37	chr14:81869200-81879200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr14:81869400-81869800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr14:81869400-81870400	Enhancers	K562	blood
40	chr14:81869400-81871200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr14:81869400-81873000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr14:81869400-81873000	Weak transcription	HSMMtube	muscle
43	chr14:81869400-81880600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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