Variant report

Variant	rs10129280
Chromosome Location	chr14:78068493-78068494
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:78068476-78068663	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:78065290..78070188-chr14:78072894..78075904,4	K562	blood:
2	chr14:78063505..78065787-chr14:78066559..78069226,2	K562	blood:
3	chr14:78068423..78071899-chr14:78079739..78082860,4	K562	blood:
4	chr14:78057510..78059603-chr14:78066224..78069062,2	MCF-7	breast:
5	chr14:78059041..78061902-chr14:78067196..78069981,2	K562	blood:

No data

Variant related genes	Relation type
SPTLC2	TF binding region
ENSG00000100596	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10137398	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10139059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10139421	0.89[YRI][hapmap]
rs10140195	0.80[ASN][1000 genomes]
rs10146161	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10873309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11626349	0.85[CHB][hapmap]
rs12587835	0.80[ASN][1000 genomes]
rs12887526	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs176901	0.81[CHB][hapmap]
rs1861942	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2267746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267747	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267748	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267754	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2299921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299922	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs2299923	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299925	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299927	0.81[CHB][hapmap]
rs2299928	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4899660	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4899661	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4903614	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58598324	0.80[ASN][1000 genomes]
rs7157356	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7158771	0.80[ASN][1000 genomes]
rs8008258	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8021376	0.94[ASN][1000 genomes]
rs8021660	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9944097	0.81[CHB][hapmap]

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

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78021800-78071600	Weak transcription	Colon Smooth Muscle	Colon
2	chr14:78047400-78070000	Weak transcription	Fetal Brain Male	brain
3	chr14:78051400-78070200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr14:78051600-78072600	Weak transcription	Psoas Muscle	Psoas
5	chr14:78055000-78081600	Weak transcription	Right Ventricle	heart
6	chr14:78056600-78072800	Weak transcription	Placenta	Placenta
7	chr14:78056800-78070000	Weak transcription	Gastric	stomach
8	chr14:78057400-78070000	Weak transcription	Spleen	Spleen
9	chr14:78057600-78081400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr14:78060200-78069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr14:78061600-78070000	Weak transcription	Esophagus	oesophagus
12	chr14:78061800-78069800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr14:78062200-78070200	Weak transcription	Ovary	ovary
14	chr14:78062800-78075000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr14:78063200-78070000	Weak transcription	Brain Germinal Matrix	brain
16	chr14:78063200-78077800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr14:78063400-78069400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr14:78063400-78069400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr14:78063400-78069800	Weak transcription	Liver	Liver
20	chr14:78063400-78070000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr14:78063400-78070200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr14:78063400-78070200	Weak transcription	Fetal Thymus	thymus
23	chr14:78063400-78081600	Weak transcription	Fetal Stomach	stomach
24	chr14:78063600-78069400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr14:78063600-78069600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr14:78063600-78070200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr14:78063800-78069400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr14:78063800-78071800	Weak transcription	Fetal Lung	lung
29	chr14:78063800-78072000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr14:78063800-78074000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr14:78063800-78074200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr14:78064600-78070600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr14:78065200-78068800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr14:78065200-78070200	Weak transcription	Fetal Intestine Large	intestine
35	chr14:78065400-78069600	Weak transcription	NHDF-Ad	bronchial
36	chr14:78065400-78070000	Weak transcription	Lung	lung
37	chr14:78065400-78071800	Weak transcription	Thymus	Thymus
38	chr14:78065600-78081400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr14:78065800-78070200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr14:78065800-78070200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr14:78065800-78071800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr14:78066000-78071600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr14:78066000-78079600	Weak transcription	Dnd41	blood
44	chr14:78066200-78069400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr14:78066200-78069600	Weak transcription	Brain Angular Gyrus	brain
46	chr14:78066200-78070200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr14:78066400-78069800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr14:78066600-78069600	Weak transcription	Primary B cells from cord blood	blood
49	chr14:78066600-78069800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr14:78066600-78070200	Weak transcription	GM12878-XiMat	blood

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