Variant report

Variant	rs2299925
Chromosome Location	chr14:78066371-78066372
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr14:78066365-78066604	K562	blood:	n/a	chr14:78066367-78066377
2	RCOR1	chr14:78066305-78066600	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:78063987..78068208-chr14:78069326..78072935,4	MCF-7	breast:
2	chr14:78065290..78070188-chr14:78072894..78075904,4	K562	blood:
3	chr14:78064657..78067063-chr14:78079647..78083000,3	MCF-7	breast:
4	chr14:78057510..78059603-chr14:78066224..78069062,2	MCF-7	breast:
5	chr14:78064498..78067393-chr14:78068632..78070407,3	K562	blood:
6	chr14:78065290..78068119-chr14:78072066..78074474,3	K562	blood:

No data

Variant related genes	Relation type
SPTLC2	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10129280	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137398	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10139059	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10140195	0.80[ASN][1000 genomes]
rs10146161	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10873309	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12587835	0.80[ASN][1000 genomes]
rs12887526	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1861942	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2267746	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267749	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267750	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267754	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2299921	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299922	0.80[ASN][1000 genomes]
rs2299923	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299924	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299928	0.96[ASN][1000 genomes]
rs4899660	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4899661	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4903614	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58598324	0.80[ASN][1000 genomes]
rs7157356	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7158771	0.80[ASN][1000 genomes]
rs8008258	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8021376	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8021660	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[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

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78021800-78068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:78021800-78071600	Weak transcription	Colon Smooth Muscle	Colon
3	chr14:78042400-78066600	Weak transcription	Fetal Brain Female	brain
4	chr14:78047400-78070000	Weak transcription	Fetal Brain Male	brain
5	chr14:78048200-78067200	Weak transcription	Hela-S3	cervix
6	chr14:78049400-78066400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr14:78051400-78070200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:78051600-78072600	Weak transcription	Psoas Muscle	Psoas
9	chr14:78055000-78081600	Weak transcription	Right Ventricle	heart
10	chr14:78056600-78072800	Weak transcription	Placenta	Placenta
11	chr14:78056800-78070000	Weak transcription	Gastric	stomach
12	chr14:78057400-78070000	Weak transcription	Spleen	Spleen
13	chr14:78057600-78081400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr14:78060200-78066800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr14:78060200-78069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr14:78061600-78070000	Weak transcription	Esophagus	oesophagus
17	chr14:78061800-78069800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr14:78062200-78068200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr14:78062200-78070200	Weak transcription	Ovary	ovary
20	chr14:78062600-78066400	Weak transcription	Fetal Intestine Small	intestine
21	chr14:78062800-78075000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr14:78063200-78070000	Weak transcription	Brain Germinal Matrix	brain
23	chr14:78063200-78077800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr14:78063400-78069400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr14:78063400-78069400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr14:78063400-78069800	Weak transcription	Liver	Liver
27	chr14:78063400-78070000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr14:78063400-78070200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr14:78063400-78070200	Weak transcription	Fetal Thymus	thymus
30	chr14:78063400-78081600	Weak transcription	Fetal Stomach	stomach
31	chr14:78063600-78066400	Weak transcription	K562	blood
32	chr14:78063600-78067800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr14:78063600-78067800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr14:78063600-78069400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr14:78063600-78069600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr14:78063600-78070200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr14:78063800-78066400	Weak transcription	Adipose Nuclei	Adipose
38	chr14:78063800-78066600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr14:78063800-78066800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr14:78063800-78067000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr14:78063800-78069400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr14:78063800-78071800	Weak transcription	Fetal Lung	lung
43	chr14:78063800-78072000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr14:78063800-78074000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr14:78063800-78074200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr14:78064000-78066400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr14:78064200-78066800	Enhancers	Primary T cells fromperipheralblood	blood
48	chr14:78064400-78066400	Weak transcription	Fetal Muscle Leg	muscle
49	chr14:78064400-78066600	Enhancers	Primary B cells from cord blood	blood
50	chr14:78064400-78067000	Enhancers	Primary B cells from peripheral blood	blood

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