Variant report

Variant	rs2299915
Chromosome Location	chr14:78014103-78014104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78013590..78016333-chr14:78173040..78175809,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ISM2-2	chr14:78013911-78014212	NONHSAT037993

Variant related genes	Relation type
ENSG00000100601	Chromatin interaction
ENSG00000119705	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10135955	0.89[CHB][hapmap]
rs10147810	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs12101129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12586959	0.96[ASN][1000 genomes]
rs12588462	0.84[CHB][hapmap]
rs12589478	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17105949	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2284230	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299911	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2299912	1.00[CEU][hapmap];0.94[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];1.00[ASN][1000 genomes]
rs2299913	1.00[CEU][hapmap];0.94[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];1.00[ASN][1000 genomes]
rs2299914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28482839	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28654332	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28676801	0.94[ASN][1000 genomes]
rs28716286	0.94[ASN][1000 genomes]
rs34359219	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55949800	0.97[ASN][1000 genomes]
rs56208416	0.89[ASN][1000 genomes]
rs61990763	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61992441	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72683251	0.82[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	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2299915	SPTLC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77970200-78047200	Weak transcription	Fetal Heart	heart
2	chr14:77972000-78018000	Weak transcription	Hela-S3	cervix
3	chr14:77978600-78014600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr14:77978800-78042200	Weak transcription	Fetal Brain Male	brain
5	chr14:77985200-78014800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr14:77985400-78015000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr14:77987400-78021000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:77987800-78014600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr14:77987800-78014600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr14:77987800-78014800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr14:77987800-78015000	Weak transcription	Thymus	Thymus
12	chr14:77987800-78015600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr14:77987800-78060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr14:77988000-78014600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr14:77988000-78014800	Weak transcription	HMEC	breast
16	chr14:77988000-78015200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr14:77988000-78015600	Weak transcription	Right Ventricle	heart
18	chr14:77988400-78029400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr14:77997800-78018800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr14:78002000-78014800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr14:78002000-78015000	Weak transcription	Lung	lung
22	chr14:78002200-78014400	Weak transcription	A549	lung
23	chr14:78002200-78020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr14:78004000-78014800	Weak transcription	Ovary	ovary
25	chr14:78004600-78014400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr14:78006800-78019000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr14:78008200-78015600	Weak transcription	NHLF	lung
28	chr14:78008200-78019000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr14:78009200-78014800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr14:78009200-78015400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr14:78009600-78014800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr14:78009600-78015600	Weak transcription	Brain Germinal Matrix	brain
33	chr14:78009600-78019400	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr14:78009600-78021200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr14:78009600-78030000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr14:78009800-78014800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr14:78009800-78050800	Weak transcription	Psoas Muscle	Psoas
38	chr14:78010000-78016400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr14:78010000-78018800	Strong transcription	NH-A	brain
40	chr14:78010000-78019800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr14:78010000-78029800	Strong transcription	Primary T cells from cord blood	blood
42	chr14:78010200-78014400	Weak transcription	Brain Substantia Nigra	brain
43	chr14:78010200-78014600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr14:78010200-78015800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr14:78010200-78019000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr14:78010200-78020400	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr14:78010200-78026800	Weak transcription	Stomach Mucosa	stomach
48	chr14:78010400-78014600	Weak transcription	Brain Angular Gyrus	brain
49	chr14:78010400-78014600	Weak transcription	GM12878-XiMat	blood
50	chr14:78010400-78015200	Weak transcription	HUVEC	blood vessel

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