Variant report

Variant	rs10139421
Chromosome Location	chr14:78064654-78064655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78063987..78068208-chr14:78069326..78072935,4	MCF-7	breast:
2	chr14:78064498..78067393-chr14:78068632..78070407,3	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10129280	0.89[YRI][hapmap]
rs10132804	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10873309	0.88[YRI][hapmap]
rs10873310	0.81[ASN][1000 genomes]
rs11159282	0.81[ASN][1000 genomes]
rs11159285	0.80[ASN][1000 genomes]
rs12432127	0.80[ASN][1000 genomes]
rs12435993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878099	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12880698	0.84[ASN][1000 genomes]
rs12881338	0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2299921	0.88[YRI][hapmap]
rs4899664	0.81[ASN][1000 genomes]
rs4903619	0.80[ASN][1000 genomes]
rs56812919	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7149026	0.80[ASN][1000 genomes]
rs7153483	0.96[ASN][1000 genomes]
rs7155602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[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
rs10139421	SPTLC2	cis	Nerve Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78013200-78066200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:78021800-78068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:78021800-78071600	Weak transcription	Colon Smooth Muscle	Colon
4	chr14:78042400-78066600	Weak transcription	Fetal Brain Female	brain
5	chr14:78047400-78070000	Weak transcription	Fetal Brain Male	brain
6	chr14:78048200-78067200	Weak transcription	Hela-S3	cervix
7	chr14:78049400-78066400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr14:78051400-78066200	Weak transcription	Pancreas	Pancrea
9	chr14:78051400-78070200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr14:78051600-78072600	Weak transcription	Psoas Muscle	Psoas
11	chr14:78055000-78081600	Weak transcription	Right Ventricle	heart
12	chr14:78056600-78072800	Weak transcription	Placenta	Placenta
13	chr14:78056800-78070000	Weak transcription	Gastric	stomach
14	chr14:78057000-78065000	Weak transcription	Lung	lung
15	chr14:78057400-78070000	Weak transcription	Spleen	Spleen
16	chr14:78057600-78081400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr14:78057800-78065000	Weak transcription	Small Intestine	intestine
18	chr14:78059000-78065800	Weak transcription	Colonic Mucosa	Colon
19	chr14:78060200-78066800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr14:78060200-78069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr14:78060400-78065000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr14:78060400-78065400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr14:78060600-78065200	Weak transcription	Fetal Kidney	kidney
24	chr14:78061200-78064800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr14:78061200-78064800	Weak transcription	Stomach Mucosa	stomach
26	chr14:78061200-78064800	Weak transcription	NHEK	skin
27	chr14:78061400-78064800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr14:78061400-78064800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr14:78061600-78070000	Weak transcription	Esophagus	oesophagus
30	chr14:78061800-78069800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr14:78062200-78064800	Weak transcription	Aorta	Aorta
32	chr14:78062200-78064800	Weak transcription	HepG2	liver
33	chr14:78062200-78066000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr14:78062200-78066200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr14:78062200-78068200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr14:78062200-78070200	Weak transcription	Ovary	ovary
37	chr14:78062600-78065000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr14:78062600-78065000	Weak transcription	HSMMtube	muscle
39	chr14:78062600-78066400	Weak transcription	Fetal Intestine Small	intestine
40	chr14:78062800-78075000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr14:78063200-78064800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr14:78063200-78065000	Weak transcription	Thymus	Thymus
43	chr14:78063200-78070000	Weak transcription	Brain Germinal Matrix	brain
44	chr14:78063200-78077800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr14:78063400-78064800	Weak transcription	Primary T cells from cord blood	blood
46	chr14:78063400-78064800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr14:78063400-78064800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr14:78063400-78065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr14:78063400-78065000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr14:78063400-78065000	Weak transcription	Brain Angular Gyrus	brain

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