Variant report

Variant	rs7252888
Chromosome Location	chr19:19628037-19628038
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19625745..19628806-chr19:19639215..19643547,5	K562	blood:
2	chr19:19626939..19628497-chr19:19651278..19652936,2	K562	blood:
3	chr19:19301631..19304213-chr19:19625502..19628076,2	MCF-7	breast:
4	chr19:19626852..19628495-chr19:19842334..19845203,2	MCF-7	breast:
5	chr19:19625365..19628497-chr19:19651436..19653967,3	K562	blood:
6	chr19:19622555..19628571-chr19:19737113..19740295,6	MCF-7	breast:
7	chr19:19625369..19628375-chr19:19648780..19652325,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064547	Chromatin interaction
ENSG00000160161	Chromatin interaction
ENSG00000105708	Chromatin interaction
ENSG00000254901	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000250067	Chromatin interaction
ENSG00000064489	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1000237	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs1009136	0.80[JPT][hapmap]
rs10282	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10401193	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]
rs10402308	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10402451	0.88[ASN][1000 genomes]
rs10402627	0.90[ASN][1000 genomes]
rs10404728	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10405625	0.84[ASN][1000 genomes]
rs10410664	0.84[ASN][1000 genomes]
rs10414830	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10419912	0.94[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10422819	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs1047361	0.88[ASN][1000 genomes]
rs1054284	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1054930	0.89[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];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12972397	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12973258	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.85[ASN][1000 genomes]
rs12975119	0.84[ASN][1000 genomes]
rs12977524	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12981405	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1465695	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1469712	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1469713	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs16996148	0.86[YRI][hapmap]
rs17288409	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1858999	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs1865034	0.88[ASN][1000 genomes]
rs2082421	0.97[ASN][1000 genomes]
rs2099333	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2099334	0.84[ASN][1000 genomes]
rs2163804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2163805	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2285628	1.00[CEU][hapmap]
rs2288852	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2301668	0.93[CEU][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs2304098	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2315610	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs28478453	0.90[ASN][1000 genomes]
rs2905424	0.80[JPT][hapmap]
rs2905425	0.80[JPT][hapmap]
rs2916073	0.84[ASN][1000 genomes]
rs2916074	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2916076	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2965180	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs2965182	0.84[ASN][1000 genomes]
rs2965183	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[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	0.81[AMR][1000 genomes];0.92[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];0.88[ASN][1000 genomes]
rs3794993	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs4808194	0.93[CEU][hapmap]
rs4808198	0.82[ASN][1000 genomes]
rs4808199	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808200	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4808202	0.84[ASN][1000 genomes]
rs4808203	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4808208	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4808950	0.87[ASN][1000 genomes]
rs4808955	0.83[ASN][1000 genomes]
rs4808957	0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4808959	0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4808960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808961	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4808964	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4808965	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4808967	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs57009615	0.84[AFR][1000 genomes]
rs60003758	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60321073	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6511036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6511038	0.87[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];0.85[ASN][1000 genomes]
rs7250658	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7250893	0.91[ASN][1000 genomes]
rs7253807	0.90[ASN][1000 genomes]
rs7254230	0.80[JPT][hapmap]
rs7256149	0.85[ASN][1000 genomes]
rs7259434	0.93[CEU][hapmap];0.84[JPT][hapmap]
rs747050	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs751856	0.88[ASN][1000 genomes]
rs751858	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs754255	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs892021	0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs892022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs968525	0.93[CEU][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs9917108	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7252888	ATP13A1	cis	multi-tissue	Pritchard
rs7252888	KIAA0892	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19626200-19628200	Active TSS	H9 Cell Line	embryonic stem cell
2	chr19:19626200-19628400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr19:19626200-19628400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr19:19626200-19628400	Active TSS	A549	lung
5	chr19:19626200-19628400	Active TSS	HSMM	muscle
6	chr19:19626400-19628200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr19:19626400-19628200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr19:19626400-19628400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr19:19626400-19628400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr19:19626600-19628200	Active TSS	H1 Cell Line	embryonic stem cell
11	chr19:19626600-19628200	Active TSS	Colonic Mucosa	Colon
12	chr19:19626600-19628200	Active TSS	Small Intestine	intestine
13	chr19:19626600-19628200	Active TSS	NHLF	lung
14	chr19:19626600-19628400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr19:19626600-19628600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:19626600-19628600	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr19:19626800-19628200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:19626800-19628200	Active TSS	Right Ventricle	heart
19	chr19:19626800-19628200	Active TSS	HMEC	breast
20	chr19:19626800-19628200	Active TSS	K562	blood
21	chr19:19626800-19628400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:19626800-19628400	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr19:19626800-19628400	Active TSS	Fetal Intestine Small	intestine
24	chr19:19626800-19628800	Active TSS	Muscle Satellite Cultured Cells	--
25	chr19:19627000-19628600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:19627200-19628200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr19:19627200-19628200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:19627200-19628200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr19:19627200-19628400	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr19:19627200-19628400	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr19:19627400-19628200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr19:19627400-19628200	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr19:19627400-19628400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:19627600-19628200	Enhancers	Fetal Heart	heart
35	chr19:19627600-19628400	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr19:19627600-19628800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr19:19627600-19629000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr19:19627600-19629000	Enhancers	Fetal Brain Male	brain
39	chr19:19627600-19629800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr19:19627600-19630000	Weak transcription	Aorta	Aorta
41	chr19:19627600-19630400	Weak transcription	Esophagus	oesophagus
42	chr19:19627600-19636200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:19627800-19628200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:19627800-19628200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:19627800-19628200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:19627800-19628200	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr19:19627800-19628200	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr19:19627800-19628200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:19627800-19628200	Flanking Active TSS	Fetal Brain Female	brain
50	chr19:19627800-19628200	Flanking Active TSS	Psoas Muscle	Psoas

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