Variant report

Variant	rs10401193
Chromosome Location	chr19:19591066-19591067
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19536218..19537719-chr19:19589722..19592712,2	K562	blood:
2	chr19:19487227..19491094-chr19:19586686..19591214,5	MCF-7	breast:
3	chr19:19590124..19591949-chr19:19596092..19599221,4	K562	blood:
4	chr19:19585281..19589285-chr19:19590381..19594944,7	K562	blood:
5	chr19:19584315..19588308-chr19:19588802..19591974,4	K562	blood:
6	chr19:19480922..19483739-chr19:19588283..19591150,2	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1000237	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs1009136	0.80[JPT][hapmap]
rs1010207	0.80[JPT][hapmap]
rs10282	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10402308	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10402451	0.91[ASN][1000 genomes]
rs10402627	0.90[ASN][1000 genomes]
rs10404728	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405625	0.87[ASN][1000 genomes]
rs10410664	0.87[ASN][1000 genomes]
rs10414830	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10419912	0.94[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10422819	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1047361	0.91[ASN][1000 genomes]
rs1054284	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1054930	0.86[ASN][1000 genomes]
rs1063966	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11085259	0.93[CEU][hapmap]
rs11669516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12972397	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12973258	0.89[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.85[ASN][1000 genomes]
rs12975119	0.87[ASN][1000 genomes]
rs12977524	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12981405	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1465695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469712	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs1469713	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs16996148	0.89[ASW][hapmap];0.84[LWK][hapmap];0.93[YRI][hapmap]
rs17288409	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1808653	0.83[ASN][1000 genomes]
rs1858999	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs1859287	0.93[CEU][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs1865034	0.91[ASN][1000 genomes]
rs2023883	0.93[CEU][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs2082421	1.00[ASN][1000 genomes]
rs2099333	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099334	0.87[ASN][1000 genomes]
rs2163804	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2163805	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2285628	1.00[CEU][hapmap]
rs2288852	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2301668	0.93[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs2301786	0.80[JPT][hapmap]
rs2304098	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2315025	0.80[JPT][hapmap]
rs2315610	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs28478453	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2905424	0.80[JPT][hapmap]
rs2905425	0.80[JPT][hapmap]
rs2916073	0.87[ASN][1000 genomes]
rs2916074	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2916076	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2965180	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs2965182	0.87[ASN][1000 genomes]
rs2965183	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2965188	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2965189	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap]
rs2965198	0.80[JPT][hapmap]
rs34277109	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs34647936	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3752151	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3764567	0.84[JPT][hapmap]
rs3794990	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3794993	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4808194	0.93[CEU][hapmap]
rs4808196	0.84[EUR][1000 genomes]
rs4808198	0.85[ASN][1000 genomes]
rs4808199	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808200	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4808202	0.87[ASN][1000 genomes]
rs4808203	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4808208	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4808950	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4808955	0.86[ASN][1000 genomes]
rs4808957	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4808959	0.94[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs4808960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808961	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4808964	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4808965	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4808967	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs60003758	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60321073	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6511036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6511038	0.90[ASN][1000 genomes]
rs6909	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7245983	0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs7250658	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250893	0.88[ASN][1000 genomes]
rs7252888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7253807	0.87[ASN][1000 genomes]
rs7254230	0.80[JPT][hapmap]
rs7256149	0.88[ASN][1000 genomes]
rs7258508	0.81[EUR][1000 genomes]
rs7259434	0.93[CEU][hapmap];0.84[JPT][hapmap]
rs747050	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs751856	0.91[ASN][1000 genomes]
rs751858	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs754255	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8108647	0.93[CEU][hapmap];0.91[MEX][hapmap]
rs892021	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs892022	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs968525	0.93[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs9917108	0.85[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	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10401193	EPS15L1	cis	cerebellum	SCAN
rs10401193	FAM125A	cis	cerebellum	SCAN
rs10401193	ATP13A1	cis	multi-tissue	Pritchard
rs10401193	KIAA0892	cis	multi-tissue	Pritchard
rs10401193	ZNF826P	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19577800-19598000	Weak transcription	Ovary	ovary
2	chr19:19579200-19598000	Weak transcription	Small Intestine	intestine
3	chr19:19579400-19599400	Weak transcription	Brain Angular Gyrus	brain
4	chr19:19579800-19593400	Weak transcription	Fetal Kidney	kidney
5	chr19:19579800-19595600	Weak transcription	Osteobl	bone
6	chr19:19579800-19595800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:19579800-19595800	Weak transcription	Colon Smooth Muscle	Colon
8	chr19:19579800-19595800	Weak transcription	HUVEC	blood vessel
9	chr19:19579800-19598600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:19579800-19599200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr19:19579800-19599800	Weak transcription	Brain Substantia Nigra	brain
12	chr19:19580600-19595200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:19580600-19597200	Weak transcription	Brain Anterior Caudate	brain
14	chr19:19580800-19593600	Strong transcription	Fetal Intestine Small	intestine
15	chr19:19581600-19595200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:19582200-19597600	Strong transcription	Dnd41	blood
17	chr19:19583600-19593200	Weak transcription	Fetal Lung	lung
18	chr19:19584200-19600000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr19:19584400-19595600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:19585400-19591200	Weak transcription	Aorta	Aorta
21	chr19:19585400-19596000	Weak transcription	HMEC	breast
22	chr19:19585600-19594200	Weak transcription	NH-A	brain
23	chr19:19585800-19591200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:19586200-19593200	Weak transcription	Fetal Heart	heart
25	chr19:19586200-19593600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:19586400-19595600	Weak transcription	NHDF-Ad	bronchial
27	chr19:19586600-19593600	Weak transcription	Psoas Muscle	Psoas
28	chr19:19586800-19594000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:19587000-19591400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr19:19587000-19595600	Weak transcription	Left Ventricle	heart
31	chr19:19587000-19599000	Weak transcription	Brain Germinal Matrix	brain
32	chr19:19587000-19599200	Weak transcription	Fetal Brain Female	brain
33	chr19:19587200-19591200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:19587200-19599600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:19587400-19593200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:19587400-19595600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr19:19587600-19591200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:19587600-19591400	Weak transcription	Adipose Nuclei	Adipose
39	chr19:19587600-19593200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr19:19587600-19593200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:19587600-19593400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr19:19587600-19593400	Weak transcription	HSMM	muscle
43	chr19:19587600-19595200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr19:19587600-19598600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:19588000-19591200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:19588000-19591400	Weak transcription	Spleen	Spleen
47	chr19:19588000-19593200	Weak transcription	Right Ventricle	heart
48	chr19:19588000-19593600	Weak transcription	NHLF	lung
49	chr19:19588000-19598400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr19:19588200-19591400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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