Variant report

Variant	rs4903586
Chromosome Location	chr14:77938633-77938634
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:77935817..77939399-chr14:77941876..77944072,3	MCF-7	breast:
2	chr14:77938499..77939140-chrX:41209394..41210229,2	MCF-7	breast:
3	chr14:77933031..77935818-chr14:77938168..77941645,3	MCF-7	breast:
4	chr14:77933444..77935805-chr14:77937175..77939418,2	MCF-7	breast:
5	chr14:77936196..77939744-chr14:77940216..77943828,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100591	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10133896	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10431633	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10431634	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10431726	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1061629	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1061638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11159259	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11159261	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11159262	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11159263	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11159264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11622359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622832	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11623826	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11624068	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11624200	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11624990	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625129	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11625365	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11627016	0.81[EUR][1000 genomes]
rs11627385	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11844594	0.89[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap]
rs12432247	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12433766	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12435136	0.89[CEU][hapmap];0.85[CHB][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap]
rs12436593	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12590773	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12878121	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12879316	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12885869	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12886224	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs147316	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs176767	0.89[CEU][hapmap]
rs176773	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs176778	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs176781	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17824034	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap]
rs17824316	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2091916	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2193595	0.89[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap]
rs2242619	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2364156	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4223	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4369582	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4575469	0.89[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap]
rs4899652	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs4899655	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4903576	0.89[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs4903579	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs4903580	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs4903583	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4903584	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6574372	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7142380	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7146595	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7146784	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7250	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs760257	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8005759	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs8006688	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8016070	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8016576	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8018513	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8018711	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs963283	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][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
rs4903586	SPTLC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 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	chr14:77935800-77939000	Weak transcription	HUVEC	blood vessel
3	chr14:77935800-77939200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr14:77935800-77940400	Weak transcription	NHEK	skin
5	chr14:77936000-77941000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr14:77936000-77944600	Weak transcription	GM12878-XiMat	blood
7	chr14:77936200-77938800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr14:77936200-77938800	Weak transcription	Brain Germinal Matrix	brain
9	chr14:77936200-77939000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:77936200-77939000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr14:77936200-77939000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr14:77936200-77939000	Weak transcription	NHLF	lung
13	chr14:77936200-77939200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:77936200-77939200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr14:77936200-77940000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr14:77936200-77940200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr14:77936200-77940200	Weak transcription	Osteobl	bone
18	chr14:77936200-77940400	Weak transcription	Fetal Kidney	kidney
19	chr14:77936200-77940800	Weak transcription	Placenta	Placenta
20	chr14:77936200-77941000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr14:77936200-77941000	Weak transcription	Fetal Lung	lung
22	chr14:77936200-77948600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr14:77936400-77939000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr14:77936400-77939000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr14:77936400-77940400	Weak transcription	Adipose Nuclei	Adipose
26	chr14:77936400-77940600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr14:77936400-77940800	Weak transcription	HepG2	liver
28	chr14:77936400-77944800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr14:77936400-77945000	Weak transcription	Gastric	stomach
30	chr14:77936400-77946000	Weak transcription	Brain Angular Gyrus	brain
31	chr14:77936600-77940800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr14:77936600-77947200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr14:77936800-77938800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr14:77936800-77938800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr14:77936800-77939600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr14:77936800-77945000	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr14:77937000-77938800	Weak transcription	Ovary	ovary
38	chr14:77937000-77939000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr14:77937000-77939800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr14:77937000-77939800	Weak transcription	Fetal Stomach	stomach
41	chr14:77937000-77945000	Weak transcription	Spleen	Spleen
42	chr14:77937200-77938800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr14:77937200-77938800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr14:77937200-77938800	Weak transcription	Primary T cells from cord blood	blood
45	chr14:77937200-77938800	Weak transcription	Liver	Liver
46	chr14:77937200-77939000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr14:77938200-77939400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr14:77938200-77939400	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr14:77938200-77939400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr14:77938600-77939200	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links