Variant report

Variant	rs1003258
Chromosome Location	chr14:81852849-81852850
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:81839869..81841648-chr14:81852139..81854142,2	K562	blood:
2	chr14:81850220..81853055-chr14:81900012..81901931,2	K562	blood:
3	chr14:81852266..81853780-chr14:81865825..81868508,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10135926	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];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10147416	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148622	0.85[YRI][hapmap]
rs12588572	0.91[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1569012	0.80[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111790	0.91[CHB][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2145123	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2371596	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2371599	0.81[CHB][hapmap]
rs2371602	0.81[CHB][hapmap]
rs28476767	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825606	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3844533	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3844534	0.91[CHB][hapmap];0.80[GIH][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3853419	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3853420	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3853421	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3915222	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4110459	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4110460	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4110462	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4275784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4290414	0.91[CHB][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4903982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6574649	0.80[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6574650	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6574651	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6574653	0.81[CHB][hapmap]
rs7153104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7153600	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7160907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72703752	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72703760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8018198	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8020806	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8022070	0.91[CHB][hapmap];0.80[GIH][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9652383	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[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
rs1003258	SPTLC2	cis	cerebellum	SCAN
rs1003258	NGB	cis	cerebellum	SCAN
rs1003258	STON2	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:81833200-81858400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr14:81834200-81859200	Weak transcription	Placenta	Placenta
3	chr14:81836400-81885800	Weak transcription	Gastric	stomach
4	chr14:81837000-81858800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr14:81837600-81856200	Weak transcription	Fetal Muscle Leg	muscle
6	chr14:81847200-81855000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr14:81847200-81855200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr14:81847200-81856800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr14:81849400-81853400	Enhancers	Fetal Kidney	kidney
10	chr14:81849600-81860600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr14:81849800-81858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr14:81850000-81855000	Weak transcription	K562	blood
13	chr14:81850000-81857400	Weak transcription	NHEK	skin
14	chr14:81850000-81858000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr14:81850400-81864000	Weak transcription	Psoas Muscle	Psoas
16	chr14:81850800-81853000	Enhancers	Brain Hippocampus Middle	brain
17	chr14:81851000-81853000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr14:81851000-81853200	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr14:81851000-81853800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr14:81851000-81856800	Weak transcription	Esophagus	oesophagus
21	chr14:81851000-81858000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr14:81851200-81853000	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr14:81851200-81853200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr14:81851200-81854000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr14:81851400-81853400	Enhancers	Brain Germinal Matrix	brain
26	chr14:81851400-81853800	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr14:81851600-81853200	Enhancers	Brain Substantia Nigra	brain
28	chr14:81851600-81854800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr14:81851600-81857600	Weak transcription	HMEC	breast
30	chr14:81851800-81853200	Enhancers	H9 Cell Line	embryonic stem cell
31	chr14:81851800-81853400	Enhancers	Brain Anterior Caudate	brain
32	chr14:81852000-81853400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr14:81852000-81853600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr14:81852000-81855000	Weak transcription	Small Intestine	intestine
35	chr14:81852000-81858600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr14:81852000-81860800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr14:81852200-81853200	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr14:81852200-81853400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr14:81852200-81853400	Enhancers	Brain Angular Gyrus	brain
40	chr14:81852200-81853800	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr14:81852200-81857400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr14:81852200-81857400	Weak transcription	NHDF-Ad	bronchial
43	chr14:81852400-81853000	Enhancers	Fetal Brain Male	brain
44	chr14:81852400-81853200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr14:81852400-81861000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr14:81852400-81862600	Weak transcription	Hela-S3	cervix
47	chr14:81852600-81853200	Enhancers	Brain Cingulate Gyrus	brain
48	chr14:81852600-81856800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr14:81852600-81859600	Weak transcription	Spleen	Spleen
50	chr14:81852600-81861600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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