Variant report

Variant	rs11625129
Chromosome Location	chr14:77938000-77938001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:77887631..77890364-chr14:77936303..77938183,2	MCF-7	breast:
2	chr14:77922040..77925665-chr14:77935403..77938131,3	MCF-7	breast:
3	chr14:77935817..77939399-chr14:77941876..77944072,3	MCF-7	breast:
4	chr14:77935677..77938460-chr14:78087456..78089168,2	MCF-7	breast:
5	chr14:77933444..77935805-chr14:77937175..77939418,2	MCF-7	breast:
6	chr14:77936196..77939744-chr14:77940216..77943828,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151445	Chromatin interaction
ENSG00000100591	Chromatin interaction
ENSG00000165555	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10431633	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10431634	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10431726	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1061629	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1061638	0.80[ASN][1000 genomes]
rs11159259	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11159261	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11159262	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11159263	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11159264	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11622359	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11622832	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11623826	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11624068	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11624200	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11624990	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11625365	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11627385	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12433766	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12436593	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12590773	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12878121	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12879316	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12885869	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12886224	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs147316	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs176773	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs176778	0.84[AMR][1000 genomes]
rs176781	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17824316	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2091916	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2242619	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2364156	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4223	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4369582	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4899655	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4903583	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4903584	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4903586	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6574372	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7142380	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7146595	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7146784	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7250	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs760257	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8006688	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8016070	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8016576	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8018513	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8018711	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs963283	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11625129	SPTLC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77926000-77939000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:77930400-77938200	Weak transcription	Fetal Heart	heart
3	chr14:77932800-77938400	Weak transcription	Psoas Muscle	Psoas
4	chr14:77935800-77938200	Weak transcription	Small Intestine	intestine
5	chr14:77935800-77938600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr14:77935800-77939000	Weak transcription	HUVEC	blood vessel
7	chr14:77935800-77939200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:77935800-77940400	Weak transcription	NHEK	skin
9	chr14:77936000-77941000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr14:77936000-77944600	Weak transcription	GM12878-XiMat	blood
11	chr14:77936200-77938000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr14:77936200-77938000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr14:77936200-77938200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr14:77936200-77938200	Weak transcription	Right Ventricle	heart
15	chr14:77936200-77938400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr14:77936200-77938600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr14:77936200-77938800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr14:77936200-77938800	Weak transcription	Brain Germinal Matrix	brain
19	chr14:77936200-77939000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr14:77936200-77939000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr14:77936200-77939000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr14:77936200-77939000	Weak transcription	NHLF	lung
23	chr14:77936200-77939200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:77936200-77939200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr14:77936200-77940000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr14:77936200-77940200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr14:77936200-77940200	Weak transcription	Osteobl	bone
28	chr14:77936200-77940400	Weak transcription	Fetal Kidney	kidney
29	chr14:77936200-77940800	Weak transcription	Placenta	Placenta
30	chr14:77936200-77941000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr14:77936200-77941000	Weak transcription	Fetal Lung	lung
32	chr14:77936200-77948600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr14:77936400-77938000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr14:77936400-77938000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr14:77936400-77938000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr14:77936400-77938000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr14:77936400-77938000	Weak transcription	HMEC	breast
38	chr14:77936400-77938200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr14:77936400-77938200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr14:77936400-77938200	Weak transcription	Primary B cells from cord blood	blood
41	chr14:77936400-77938200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr14:77936400-77938200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr14:77936400-77938200	Weak transcription	Brain Anterior Caudate	brain
44	chr14:77936400-77938600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr14:77936400-77938600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr14:77936400-77938600	Weak transcription	Fetal Brain Female	brain
47	chr14:77936400-77938600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr14:77936400-77938600	Weak transcription	Thymus	Thymus
49	chr14:77936400-77938600	Weak transcription	Dnd41	blood
50	chr14:77936400-77939000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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