Variant report

Variant	rs12590773
Chromosome Location	chr14:77933986-77933987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:77923271..77925943-chr14:77932177..77936062,3	K562	blood:
2	chr14:77921860..77928400-chr14:77931824..77937732,8	MCF-7	breast:
3	chr14:77924775..77928699-chr14:77931957..77935059,4	K562	blood:

Variant related genes	Relation type
ENSG00000151445	Chromatin interaction
ENSG00000100591	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10431633	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10431634	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10431726	0.88[AMR][1000 genomes]
rs1061629	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1061638	1.00[ASN][1000 genomes]
rs11159258	0.85[EUR][1000 genomes]
rs11159259	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11159261	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11159262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11159263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11159264	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622359	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11622832	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623826	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11624068	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11624990	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11625129	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11625365	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11627016	0.86[EUR][1000 genomes]
rs11627385	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12433766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12436593	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12878121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12879316	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12885869	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12886224	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs147316	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs176768	0.84[EUR][1000 genomes]
rs176772	0.85[EUR][1000 genomes]
rs176773	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs176778	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs176781	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17824034	0.84[EUR][1000 genomes]
rs17824316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091916	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2242619	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2364156	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35881785	0.80[EUR][1000 genomes]
rs4223	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4369582	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4899654	0.83[EUR][1000 genomes]
rs4899655	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4903583	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4903584	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4903586	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6574372	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7142380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760257	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8005759	0.86[EUR][1000 genomes]
rs8006688	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8016070	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8016576	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8018513	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8018711	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs963283	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041985	chr14:77877421-77936969	Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12590773	SPTLC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77925600-77936600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:77925800-77936400	Strong transcription	Fetal Muscle Trunk	muscle
3	chr14:77926000-77936200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr14:77926000-77936200	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr14:77926000-77936400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr14:77926000-77936800	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr14:77926000-77936800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr14:77926000-77939000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr14:77926200-77935400	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr14:77926200-77935600	Strong transcription	HSMM	muscle
11	chr14:77926200-77935800	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr14:77926200-77936000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr14:77926200-77936000	Strong transcription	NHDF-Ad	bronchial
14	chr14:77926200-77936200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:77926200-77936200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr14:77926200-77936200	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr14:77926200-77936200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr14:77926200-77936200	Strong transcription	Fetal Intestine Large	intestine
19	chr14:77926200-77936200	Strong transcription	Placenta	Placenta
20	chr14:77926200-77936200	Strong transcription	Fetal Thymus	thymus
21	chr14:77926200-77936200	Strong transcription	Lung	lung
22	chr14:77926200-77936200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr14:77926200-77936400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr14:77926200-77936400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr14:77926200-77936400	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr14:77926200-77936400	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr14:77926200-77936600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr14:77926200-77936800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr14:77926200-77936800	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr14:77926200-77937000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr14:77926200-77937000	Strong transcription	Fetal Stomach	stomach
32	chr14:77926200-77937000	Strong transcription	Ovary	ovary
33	chr14:77926400-77935800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr14:77926400-77935800	Strong transcription	Fetal Intestine Small	intestine
35	chr14:77926400-77936000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr14:77926400-77936000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr14:77926400-77936000	Strong transcription	HSMMtube	muscle
38	chr14:77926400-77936200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr14:77926400-77936200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr14:77926400-77936200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr14:77926400-77936200	Strong transcription	Fetal Kidney	kidney
42	chr14:77926400-77936200	Strong transcription	Osteobl	bone
43	chr14:77926400-77936400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr14:77926400-77936400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr14:77926400-77936400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr14:77926400-77936400	Strong transcription	Adipose Nuclei	Adipose
47	chr14:77926400-77936400	Strong transcription	Fetal Brain Female	brain
48	chr14:77926400-77936400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr14:77926400-77936600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr14:77926400-77936600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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