Variant report

Variant	rs4903620
Chromosome Location	chr14:78108110-78108111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10139421	0.81[JPT][hapmap]
rs10873310	0.96[ASN][1000 genomes]
rs11159282	0.96[ASN][1000 genomes]
rs11159285	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11620917	0.89[CHD][hapmap]
rs12050437	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12050439	1.00[ASN][1000 genomes]
rs12432127	0.99[ASN][1000 genomes]
rs12435993	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs12586560	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12590445	0.93[ASN][1000 genomes]
rs12590759	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12590776	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878099	0.82[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs12879146	0.98[ASN][1000 genomes]
rs12880698	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12881338	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12881530	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.96[ASN][1000 genomes]
rs12886970	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12889224	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12898009	1.00[CHB][hapmap];0.81[JPT][hapmap];0.98[ASN][1000 genomes]
rs2886123	0.89[CHD][hapmap]
rs34140630	0.98[ASN][1000 genomes]
rs34567686	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35636868	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4243658	0.85[CHD][hapmap]
rs4899664	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4903619	0.99[ASN][1000 genomes]
rs56812919	0.82[ASN][1000 genomes]
rs67838524	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71428789	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7149026	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7153483	0.82[ASN][1000 genomes]
rs7155602	0.87[CEU][hapmap];0.81[ASN][1000 genomes]
rs8004037	0.98[ASN][1000 genomes]
rs8021379	0.89[CHD][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4903620	SPTLC2	cis	parietal	SCAN
rs4903620	SPTLC2	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78107400-78108200	Enhancers	Small Intestine	intestine
2	chr14:78107400-78108800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr14:78107400-78109000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr14:78107400-78109000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr14:78107400-78109000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr14:78107600-78108200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr14:78107600-78108200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr14:78107600-78108200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr14:78107600-78108200	Enhancers	Gastric	stomach
10	chr14:78107600-78108200	Enhancers	Pancreas	Pancrea
11	chr14:78107600-78108200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr14:78107600-78108200	Enhancers	HSMM	muscle
13	chr14:78107600-78108400	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr14:78107600-78108400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr14:78107600-78108800	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr14:78107600-78108800	Flanking Active TSS	GM12878-XiMat	blood
17	chr14:78107600-78109000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr14:78107600-78109000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr14:78107600-78109000	Active TSS	Colon Smooth Muscle	Colon
20	chr14:78107600-78109000	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr14:78107600-78109000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr14:78107600-78109000	Flanking Active TSS	Osteobl	bone
23	chr14:78107800-78108200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr14:78107800-78108200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr14:78107800-78108200	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr14:78107800-78108200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr14:78107800-78108200	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr14:78107800-78108200	Flanking Active TSS	Rectal Smooth Muscle	rectum
29	chr14:78107800-78108200	Flanking Active TSS	Thymus	Thymus
30	chr14:78107800-78108200	Enhancers	Spleen	Spleen
31	chr14:78107800-78108200	Enhancers	HepG2	liver
32	chr14:78107800-78108600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr14:78107800-78108600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr14:78107800-78108600	Flanking Active TSS	Liver	Liver
35	chr14:78107800-78108600	Active TSS	Brain Hippocampus Middle	brain
36	chr14:78107800-78108600	Flanking Active TSS	Stomach Mucosa	stomach
37	chr14:78107800-78108600	Flanking Active TSS	NH-A	brain
38	chr14:78107800-78108800	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr14:78107800-78108800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr14:78107800-78108800	Active TSS	Brain Substantia Nigra	brain
41	chr14:78107800-78108800	Enhancers	Fetal Heart	heart
42	chr14:78107800-78108800	Active TSS	Fetal Kidney	kidney
43	chr14:78107800-78108800	Flanking Active TSS	Placenta	Placenta
44	chr14:78107800-78108800	Flanking Active TSS	Fetal Thymus	thymus
45	chr14:78107800-78109000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr14:78107800-78109000	Active TSS	Brain Cingulate Gyrus	brain
47	chr14:78107800-78109000	Flanking Active TSS	Colonic Mucosa	Colon
48	chr14:78107800-78109000	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr14:78107800-78109000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr14:78107800-78109000	Active TSS	Ovary	ovary

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