Variant report

Variant	rs8006300
Chromosome Location	chr14:72050162-72050163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr14:72049280-72050241	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr14:72050089-72050726	SH-SY5Y	brain:	n/a	n/a
3	EP300	chr14:72049038-72051792	SK-N-SH	brain:	n/a	chr14:72049524-72049538
4	PBX3	chr14:72049334-72050205	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr14:72049265-72050460	SK-N-SH	brain:	n/a	n/a
6	MYC	chr14:72050086-72050381	NB4	blood:	n/a	n/a
7	EP300	chr14:72049283-72050362	SK-N-SH	brain:	n/a	chr14:72049524-72049538
8	PBX3	chr14:72049250-72050294	SK-N-SH	brain:	n/a	n/a
9	TCF12	chr14:72049178-72050360	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr14:72049144-72050403	SK-N-SH	brain:	n/a	chr14:72049308-72049329 chr14:72049316-72049333 chr14:72049315-72049322 chr14:72049314-72049324 chr14:72049315-72049322 chr14:72049315-72049322 chr14:72049311-72049327
11	GATA3	chr14:72049159-72050777	SK-N-SH	brain:	n/a	chr14:72049308-72049329 chr14:72049316-72049333 chr14:72049315-72049322 chr14:72049314-72049324 chr14:72049315-72049322 chr14:72049315-72049322 chr14:72049311-72049327
12	SPI1	chr14:72050057-72050431	HL-60	blood:	n/a	chr14:72050243-72050252
13	RFX5	chr14:72048357-72054524	SK-N-SH	brain:	n/a	chr14:72050604-72050613 chr14:72051979-72051987 chr14:72050601-72050615

Variant related genes	Relation type
SIPA1L1	TF binding region

Extended variants
information (count: 115 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10135680	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10138557	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10139519	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs1029570	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10483836	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11848785	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127	0.87[EUR][1000 genomes]
rs12433040	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12878989	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12879243	0.80[EUR][1000 genomes]
rs12880188	0.95[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12880291	0.87[EUR][1000 genomes]
rs12880611	0.81[EUR][1000 genomes]
rs12881957	0.81[EUR][1000 genomes]
rs12885344	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12887261	0.87[EUR][1000 genomes]
rs12889866	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs12892512	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12894016	0.80[EUR][1000 genomes]
rs12896900	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs12896986	0.81[EUR][1000 genomes]
rs14030	0.87[EUR][1000 genomes]
rs17178206	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs17178234	0.81[EUR][1000 genomes]
rs17178387	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17767523	0.81[EUR][1000 genomes]
rs17767553	0.91[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs17767680	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17767686	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1859643	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1981588	0.91[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2108049	0.81[EUR][1000 genomes]
rs2108057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2109276	0.81[EUR][1000 genomes]
rs2190240	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2214836	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2286136	0.82[CHD][hapmap]
rs2332638	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2332640	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2332641	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2877729	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs28859432	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs33994051	0.81[EUR][1000 genomes]
rs34169215	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34281934	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34320622	0.81[EUR][1000 genomes]
rs34347034	0.80[EUR][1000 genomes]
rs34388001	0.87[EUR][1000 genomes]
rs34454371	0.80[EUR][1000 genomes]
rs34469007	0.81[EUR][1000 genomes]
rs34480562	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34991781	0.86[EUR][1000 genomes]
rs34993988	0.81[EUR][1000 genomes]
rs35231795	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35415083	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35589413	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35613269	0.81[EUR][1000 genomes]
rs35620527	0.87[EUR][1000 genomes]
rs35625243	0.86[EUR][1000 genomes]
rs35760654	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35831373	0.86[EUR][1000 genomes]
rs35866366	0.84[EUR][1000 genomes]
rs35971049	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36052007	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36072220	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3784062	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3784064	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3784066	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3825719	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4899398	0.91[CEU][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4902938	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4902941	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55883127	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56180634	0.94[EUR][1000 genomes]
rs56407721	0.81[EUR][1000 genomes]
rs61989367	0.81[EUR][1000 genomes]
rs61989373	0.81[EUR][1000 genomes]
rs61989374	0.81[EUR][1000 genomes]
rs61989377	0.80[EUR][1000 genomes]
rs61989379	0.87[EUR][1000 genomes]
rs61989382	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61989383	0.90[EUR][1000 genomes]
rs61989386	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61991243	0.84[EUR][1000 genomes]
rs61991246	0.84[EUR][1000 genomes]
rs61991249	0.84[EUR][1000 genomes]
rs61991255	0.81[EUR][1000 genomes]
rs6574015	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6574016	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66645707	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67489015	0.81[EUR][1000 genomes]
rs7140501	0.96[CEU][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7142343	0.91[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7144299	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7144829	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7152674	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7152842	0.84[EUR][1000 genomes]
rs7154841	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7156313	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7157241	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs722633	0.81[EUR][1000 genomes]
rs725673	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs757850	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8003478	0.83[EUR][1000 genomes]
rs8008605	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8010616	0.85[EUR][1000 genomes]
rs8013161	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8014349	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8015644	0.83[EUR][1000 genomes]
rs8017775	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8019721	0.84[EUR][1000 genomes]
rs9323561	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9672060	0.96[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][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	nsv498021	chr14:71874708-72128721	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3398985	chr14:71927884-72404676	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8006300	PCNX	cis	cerebellum	SCAN
rs8006300	MAP3K9	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72024400-72052400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr14:72031000-72052600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr14:72035200-72053400	Weak transcription	Spleen	Spleen
4	chr14:72035600-72054600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr14:72037200-72051000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr14:72039400-72064400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr14:72041200-72050800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr14:72041200-72052600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr14:72041400-72052600	Weak transcription	Primary B cells from cord blood	blood
10	chr14:72041400-72054200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr14:72042000-72058400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr14:72042000-72058600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr14:72042000-72058800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr14:72042000-72069400	Weak transcription	Lung	lung
15	chr14:72042200-72054400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr14:72042200-72058400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr14:72042200-72058600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr14:72042200-72058600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr14:72043000-72054400	Weak transcription	GM12878-XiMat	blood
20	chr14:72043200-72052200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr14:72043200-72052600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr14:72043200-72052600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr14:72043400-72050200	Weak transcription	Brain Substantia Nigra	brain
24	chr14:72043400-72050600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr14:72043400-72059200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr14:72047000-72050400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr14:72047000-72052400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr14:72047200-72050600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr14:72047600-72051000	Enhancers	Osteobl	bone
30	chr14:72048600-72050200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr14:72048600-72050200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr14:72048600-72051600	Enhancers	HSMM	muscle
33	chr14:72048600-72052600	Enhancers	NHDF-Ad	bronchial
34	chr14:72048800-72050200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr14:72048800-72050200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr14:72048800-72051400	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr14:72048800-72052400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr14:72049200-72050200	Enhancers	NHLF	lung
39	chr14:72049200-72050800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr14:72049200-72051000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr14:72049200-72051000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr14:72049200-72051200	Enhancers	HSMMtube	muscle
43	chr14:72049200-72052400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr14:72049400-72050600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr14:72049400-72051000	Enhancers	Colon Smooth Muscle	Colon
46	chr14:72049400-72053000	Weak transcription	Fetal Kidney	kidney
47	chr14:72049600-72050200	Enhancers	Fetal Heart	heart
48	chr14:72049600-72050200	Enhancers	Rectal Smooth Muscle	rectum
49	chr14:72049600-72050200	Enhancers	Stomach Smooth Muscle	stomach
50	chr14:72049600-72051000	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links