Variant report

Variant	rs28527479
Chromosome Location	chr14:78010267-78010268
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78009315..78010899-chr14:78010938..78012880,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10151907	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17105922	1.00[ASN][1000 genomes]
rs17105930	1.00[ASN][1000 genomes]
rs17105935	1.00[ASN][1000 genomes]
rs17105954	1.00[ASN][1000 genomes]
rs28417590	1.00[ASN][1000 genomes]
rs28584839	1.00[ASN][1000 genomes]
rs28608714	1.00[ASN][1000 genomes]
rs28628767	1.00[ASN][1000 genomes]
rs28677959	1.00[ASN][1000 genomes]
rs28708472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28714070	1.00[ASN][1000 genomes]
rs28719093	1.00[ASN][1000 genomes]
rs55732483	1.00[ASN][1000 genomes]
rs56138064	1.00[ASN][1000 genomes]
rs56192928	1.00[ASN][1000 genomes]
rs56276583	1.00[ASN][1000 genomes]
rs56327799	1.00[ASN][1000 genomes]
rs56361144	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7144024	1.00[ASN][1000 genomes]
rs7145386	1.00[ASN][1000 genomes]
rs7160438	0.80[EUR][1000 genomes]
rs73303254	1.00[ASN][1000 genomes]
rs74063289	1.00[ASN][1000 genomes]
rs8018049	1.00[ASN][1000 genomes]
rs8019658	1.00[ASN][1000 genomes]
rs9323645	1.00[ASN][1000 genomes]
rs9806055	1.00[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
rs28527479	SPTLC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 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	chr14:77978000-78013400	Weak transcription	NHDF-Ad	bronchial
4	chr14:77978600-78014600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr14:77978800-78042200	Weak transcription	Fetal Brain Male	brain
6	chr14:77979000-78013800	Weak transcription	Pancreas	Pancrea
7	chr14:77985200-78014800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr14:77985400-78015000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr14:77986200-78013800	Weak transcription	Esophagus	oesophagus
10	chr14:77987400-78021000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr14:77987600-78010600	Weak transcription	Left Ventricle	heart
12	chr14:77987800-78013400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr14:77987800-78013600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr14:77987800-78013800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:77987800-78014600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr14:77987800-78014600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr14:77987800-78014800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr14:77987800-78015000	Weak transcription	Thymus	Thymus
19	chr14:77987800-78015600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr14:77987800-78060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr14:77988000-78010600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr14:77988000-78010800	Weak transcription	Dnd41	blood
23	chr14:77988000-78013800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr14:77988000-78013800	Weak transcription	Colonic Mucosa	Colon
25	chr14:77988000-78014600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr14:77988000-78014800	Weak transcription	HMEC	breast
27	chr14:77988000-78015200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr14:77988000-78015600	Weak transcription	Right Ventricle	heart
29	chr14:77988400-78013000	Weak transcription	Small Intestine	intestine
30	chr14:77988400-78013800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr14:77988400-78029400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr14:77988600-78013400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr14:77990000-78010600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr14:77990400-78010800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr14:77997800-78018800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr14:78001400-78014000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr14:78001600-78010400	Weak transcription	Fetal Intestine Large	intestine
38	chr14:78001800-78014000	Weak transcription	Fetal Intestine Small	intestine
39	chr14:78002000-78010400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr14:78002000-78010600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr14:78002000-78011200	Weak transcription	Liver	Liver
42	chr14:78002000-78014800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr14:78002000-78015000	Weak transcription	Lung	lung
44	chr14:78002200-78014400	Weak transcription	A549	lung
45	chr14:78002200-78020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr14:78002400-78010600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr14:78002400-78013600	Weak transcription	NHEK	skin
48	chr14:78004000-78014800	Weak transcription	Ovary	ovary
49	chr14:78004600-78014400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr14:78006600-78010400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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