Variant report

Variant	rs17235614
Chromosome Location	chr13:97953193-97953194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:97944192..97946659-chr13:97951933..97954715,2	MCF-7	breast:
2	chr13:97946659..97950744-chr13:97950983..97954750,4	MCF-7	breast:
3	chr13:97940763..97942613-chr13:97953141..97954942,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11843522	0.82[YRI][hapmap]
rs12864731	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1328834	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs16954000	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs17301362	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs35039622	0.83[ASN][1000 genomes]
rs35538229	0.83[ASN][1000 genomes]
rs56940858	0.83[ASN][1000 genomes]
rs58421118	0.81[ASN][1000 genomes]
rs61255793	0.83[ASN][1000 genomes]
rs7999038	0.83[ASN][1000 genomes]
rs9513227	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs9513228	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9513229	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9513230	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9513231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9513232	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9516891	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9516895	0.85[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9516896	1.00[CHB][hapmap]
rs9516897	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9516898	0.83[ASN][1000 genomes]
rs9516899	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs953504	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];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	nsv1045777	chr13:97875574-97955134	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv832694	chr13:97930561-98137882	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17235614	ATP13A1	trans	brain	seeQTL
rs17235614	HSPA6	trans	brain	seeQTL
rs17235614	MRPL32	trans	brain	seeQTL
rs17235614	APOL2	trans	brain	seeQTL
rs17235614	THAP7	trans	brain	seeQTL
rs17235614	PEX14	trans	brain	seeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:97914200-97960200	Weak transcription	Fetal Brain Male	brain
2	chr13:97925800-97987200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr13:97929400-97955000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr13:97929600-97953400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr13:97929800-97953200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr13:97929800-97953400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr13:97931000-97953600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr13:97933000-97953600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr13:97933200-97970400	Weak transcription	Placenta	Placenta
10	chr13:97933600-97953600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr13:97934000-97954400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr13:97935600-97954800	Weak transcription	Colonic Mucosa	Colon
13	chr13:97942800-97995200	Weak transcription	Thymus	Thymus
14	chr13:97943400-97953600	Weak transcription	Esophagus	oesophagus
15	chr13:97943400-97957800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr13:97946400-97956400	Enhancers	Brain Cingulate Gyrus	brain
17	chr13:97946600-97956400	Enhancers	Brain Anterior Caudate	brain
18	chr13:97947000-97953200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr13:97947400-97954400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr13:97947800-97953400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr13:97947800-97953600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr13:97948000-97953400	Weak transcription	Spleen	Spleen
23	chr13:97948000-97954400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr13:97948000-97958600	Weak transcription	Fetal Stomach	stomach
25	chr13:97948200-97958200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr13:97948600-97956400	Enhancers	Brain Angular Gyrus	brain
27	chr13:97948600-97958400	Weak transcription	HSMMtube	muscle
28	chr13:97948600-97971600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr13:97948800-97954200	Weak transcription	Fetal Heart	heart
30	chr13:97949200-97953200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr13:97949200-97953600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr13:97949400-97953800	Weak transcription	Hela-S3	cervix
33	chr13:97949800-97953800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr13:97949800-97954000	Weak transcription	Primary T cells from cord blood	blood
35	chr13:97949800-97955800	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr13:97950000-97953200	Weak transcription	Right Atrium	heart
37	chr13:97950000-97953400	Weak transcription	Adipose Nuclei	Adipose
38	chr13:97950000-97958400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr13:97950000-97958400	Weak transcription	Fetal Intestine Small	intestine
40	chr13:97950000-97971200	Weak transcription	Stomach Mucosa	stomach
41	chr13:97950200-97953200	Strong transcription	Fetal Lung	lung
42	chr13:97950200-97953400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr13:97950200-97953600	Weak transcription	Fetal Muscle Leg	muscle
44	chr13:97950200-97961000	Weak transcription	K562	blood
45	chr13:97950200-97965200	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr13:97950400-97953400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr13:97950800-97965200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr13:97951000-97953400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr13:97951200-97953200	Weak transcription	Gastric	stomach
50	chr13:97951200-97953600	Weak transcription	Lung	lung

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