Variant report

Variant	rs17825181
Chromosome Location	chr14:78108274-78108275
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11620917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11621029	0.98[ASN][1000 genomes]
rs11625133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11625369	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12589812	0.93[ASN][1000 genomes]
rs2886123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34856099	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4243658	0.88[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs8003416	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8017748	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8021379	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv2757575	chr14:78104897-78212462	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34940	chr14:78104897-78222798	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv521287	chr14:78108003-78211225	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17825181	SPTLC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78107400-78108800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr14:78107400-78109000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr14:78107400-78109000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr14:78107400-78109000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr14:78107600-78108400	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr14:78107600-78108400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
7	chr14:78107600-78108800	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr14:78107600-78108800	Flanking Active TSS	GM12878-XiMat	blood
9	chr14:78107600-78109000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr14:78107600-78109000	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr14:78107600-78109000	Active TSS	Colon Smooth Muscle	Colon
12	chr14:78107600-78109000	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr14:78107600-78109000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr14:78107600-78109000	Flanking Active TSS	Osteobl	bone
15	chr14:78107800-78108600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr14:78107800-78108600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr14:78107800-78108600	Flanking Active TSS	Liver	Liver
18	chr14:78107800-78108600	Active TSS	Brain Hippocampus Middle	brain
19	chr14:78107800-78108600	Flanking Active TSS	Stomach Mucosa	stomach
20	chr14:78107800-78108600	Flanking Active TSS	NH-A	brain
21	chr14:78107800-78108800	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr14:78107800-78108800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr14:78107800-78108800	Active TSS	Brain Substantia Nigra	brain
24	chr14:78107800-78108800	Enhancers	Fetal Heart	heart
25	chr14:78107800-78108800	Active TSS	Fetal Kidney	kidney
26	chr14:78107800-78108800	Flanking Active TSS	Placenta	Placenta
27	chr14:78107800-78108800	Flanking Active TSS	Fetal Thymus	thymus
28	chr14:78107800-78109000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr14:78107800-78109000	Active TSS	Brain Cingulate Gyrus	brain
30	chr14:78107800-78109000	Flanking Active TSS	Colonic Mucosa	Colon
31	chr14:78107800-78109000	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr14:78107800-78109000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr14:78107800-78109000	Active TSS	Ovary	ovary
34	chr14:78108000-78108400	Flanking Active TSS	Fetal Stomach	stomach
35	chr14:78108000-78108400	Flanking Active TSS	Left Ventricle	heart
36	chr14:78108000-78108400	Flanking Active TSS	Psoas Muscle	Psoas
37	chr14:78108000-78108400	Flanking Active TSS	Right Atrium	heart
38	chr14:78108000-78108400	Flanking Active TSS	Right Ventricle	heart
39	chr14:78108000-78108400	Flanking Active TSS	NHLF	lung
40	chr14:78108000-78108600	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr14:78108000-78108600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr14:78108000-78108600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr14:78108000-78108600	Active TSS	Fetal Brain Female	brain
44	chr14:78108000-78108600	Active TSS	Fetal Lung	lung
45	chr14:78108000-78108600	Flanking Active TSS	Lung	lung
46	chr14:78108000-78108800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr14:78108000-78108800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr14:78108000-78108800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr14:78108000-78108800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr14:78108000-78108800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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