Variant report

Variant	rs4899398
Chromosome Location	chr14:72083441-72083442
allele	A/G
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	USF2	chr14:72083364-72083547	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:72079358..72081183-chr14:72081812..72085209,3	MCF-7	breast:
2	chr14:72076596..72079373-chr14:72082205..72083777,2	K562	blood:

Variant related genes	Relation type
SIPA1L1	TF binding region

Extended variants
information (count: 135 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10133626	1.00[JPT][hapmap]
rs10135680	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10138557	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10139519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1029570	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10483836	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10873246	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11848785	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1204995	0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1204996	1.00[JPT][hapmap]
rs12127	0.81[EUR][1000 genomes]
rs12433040	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12879243	0.88[EUR][1000 genomes]
rs12880188	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12880291	0.81[EUR][1000 genomes]
rs12880611	0.89[EUR][1000 genomes]
rs12881643	0.86[EUR][1000 genomes]
rs12881957	0.86[EUR][1000 genomes]
rs12885344	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12887261	0.81[EUR][1000 genomes]
rs12889866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs12892512	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12894016	0.88[EUR][1000 genomes]
rs12896900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12896986	0.89[EUR][1000 genomes]
rs14030	0.81[EUR][1000 genomes]
rs17178206	0.89[EUR][1000 genomes]
rs17178234	0.89[EUR][1000 genomes]
rs17178387	0.88[EUR][1000 genomes]
rs17767499	0.86[EUR][1000 genomes]
rs17767523	0.89[EUR][1000 genomes]
rs17767553	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs17767680	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17767686	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1859643	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1981588	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2108049	0.89[EUR][1000 genomes]
rs2108057	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2109276	0.89[EUR][1000 genomes]
rs2190240	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2214836	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286136	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2332638	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2332640	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2332641	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2877729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs28859432	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33994051	0.89[EUR][1000 genomes]
rs34169215	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34176710	0.88[EUR][1000 genomes]
rs34281934	0.88[EUR][1000 genomes]
rs34320622	0.89[EUR][1000 genomes]
rs34347034	0.88[EUR][1000 genomes]
rs34388001	0.81[EUR][1000 genomes]
rs34454371	0.88[EUR][1000 genomes]
rs34469007	0.89[EUR][1000 genomes]
rs34480562	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34524083	0.86[EUR][1000 genomes]
rs34528131	0.86[EUR][1000 genomes]
rs34991781	0.80[EUR][1000 genomes]
rs34993988	0.86[EUR][1000 genomes]
rs35051046	0.86[EUR][1000 genomes]
rs35231795	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35415083	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35468256	0.86[EUR][1000 genomes]
rs35589413	0.87[EUR][1000 genomes]
rs35609708	0.82[EUR][1000 genomes]
rs35613269	0.89[EUR][1000 genomes]
rs35620527	0.81[EUR][1000 genomes]
rs35680546	0.88[EUR][1000 genomes]
rs35760654	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35831373	0.80[EUR][1000 genomes]
rs35854505	0.86[EUR][1000 genomes]
rs35866366	0.81[EUR][1000 genomes]
rs35971049	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36052007	0.88[EUR][1000 genomes]
rs36072220	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36093218	0.88[EUR][1000 genomes]
rs3784062	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3784064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3784066	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3825719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4140797	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4319698	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902938	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4902941	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902942	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55883127	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56180634	0.85[EUR][1000 genomes]
rs56407721	0.86[EUR][1000 genomes]
rs61989367	0.89[EUR][1000 genomes]
rs61989373	0.89[EUR][1000 genomes]
rs61989374	0.89[EUR][1000 genomes]
rs61989377	0.88[EUR][1000 genomes]
rs61989379	0.81[EUR][1000 genomes]
rs61989382	0.88[EUR][1000 genomes]
rs61989383	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61989386	0.88[EUR][1000 genomes]
rs61989417	0.93[AFR][1000 genomes]
rs61991247	0.86[EUR][1000 genomes]
rs61991248	0.86[EUR][1000 genomes]
rs61991250	0.86[EUR][1000 genomes]
rs61991254	0.85[EUR][1000 genomes]
rs61991255	0.89[EUR][1000 genomes]
rs6574015	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6574016	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66645707	0.88[EUR][1000 genomes]
rs67489015	0.86[EUR][1000 genomes]
rs7140501	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7142343	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7144299	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7144829	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7145755	0.86[EUR][1000 genomes]
rs7147668	0.86[EUR][1000 genomes]
rs7148679	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7152674	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7154787	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7154841	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7156313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7156460	0.86[EUR][1000 genomes]
rs7157241	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs722633	0.89[EUR][1000 genomes]
rs725673	0.89[EUR][1000 genomes]
rs757850	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8003478	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8006300	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]
rs8008605	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8010616	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8013161	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8014349	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8017775	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9323561	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9672060	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4899398	SIPA1L1	cis	cerebellum	SCAN
rs4899398	PCNX	cis	parietal	SCAN
rs4899398	PCNX	cis	cerebellum	SCAN
rs4899398	COQ6	cis	parietal	SCAN
rs4899398	SMOC1	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72053400-72098800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:72055200-72087800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:72059000-72098600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr14:72059400-72088000	Weak transcription	NHLF	lung
5	chr14:72059800-72085600	Weak transcription	NH-A	brain
6	chr14:72059800-72087600	Weak transcription	Hela-S3	cervix
7	chr14:72063200-72087200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr14:72064800-72084800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:72064800-72085000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr14:72065000-72087200	Weak transcription	NHEK	skin
11	chr14:72065200-72085400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr14:72065400-72085600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr14:72065800-72085600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr14:72065800-72089600	Weak transcription	HSMMtube	muscle
15	chr14:72067400-72084600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr14:72067400-72084600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr14:72069400-72083800	Weak transcription	Primary B cells from cord blood	blood
18	chr14:72071400-72085400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr14:72072600-72087000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr14:72072600-72090600	Weak transcription	Fetal Intestine Large	intestine
21	chr14:72072600-72103600	Weak transcription	Left Ventricle	heart
22	chr14:72072800-72087200	Weak transcription	Aorta	Aorta
23	chr14:72073200-72085400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr14:72073200-72085600	Weak transcription	HSMM	muscle
25	chr14:72073200-72087200	Weak transcription	Fetal Intestine Small	intestine
26	chr14:72073200-72087400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr14:72073200-72090600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr14:72073200-72099200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr14:72073200-72137800	Weak transcription	Esophagus	oesophagus
30	chr14:72073400-72090600	Weak transcription	Pancreas	Pancrea
31	chr14:72073400-72093600	Weak transcription	Gastric	stomach
32	chr14:72073400-72111000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr14:72073600-72085800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr14:72074000-72085800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr14:72074000-72089800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr14:72074000-72090600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr14:72074000-72090600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr14:72074400-72083600	Weak transcription	Thymus	Thymus
39	chr14:72074400-72085400	Weak transcription	Primary T cells from cord blood	blood
40	chr14:72075000-72087600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr14:72075000-72087800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr14:72075200-72085800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr14:72075200-72087200	Weak transcription	Dnd41	blood
44	chr14:72075200-72092600	Weak transcription	Brain Substantia Nigra	brain
45	chr14:72075200-72093800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr14:72075200-72106800	Weak transcription	Brain Hippocampus Middle	brain
47	chr14:72077000-72084400	Weak transcription	Osteobl	bone
48	chr14:72077600-72085800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr14:72077800-72085800	Weak transcription	Brain Angular Gyrus	brain
50	chr14:72077800-72088600	Weak transcription	Brain Germinal Matrix	brain

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