Variant report

Variant	rs9316367
Chromosome Location	chr13:48810789-48810790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:48809762..48812244-chr13:48818383..48819991,2	K562	blood:
2	chr13:48808662..48812732-chr13:48820679..48824988,4	K562	blood:
3	chr13:48803757..48809033-chr13:48809443..48816513,10	MCF-7	breast:
4	chr13:48807837..48812135-chr13:48876736..48879539,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139687	Chromatin interaction
ENSG00000136156	Chromatin interaction
ENSG00000231473	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10219833	0.87[EUR][1000 genomes]
rs12100135	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12583516	0.82[ASN][1000 genomes]
rs12871662	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12871740	0.86[EUR][1000 genomes]
rs12875750	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1573601	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1886795	0.87[EUR][1000 genomes]
rs1894255	0.85[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.90[TSI][hapmap]
rs1925744	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1925745	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1981434	0.90[CEU][hapmap]
rs198561	0.83[EUR][1000 genomes]
rs198563	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs198604	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs198607	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap]
rs198612	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs198619	0.90[CEU][hapmap]
rs198634	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2243461	0.86[EUR][1000 genomes]
rs2243626	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs2248488	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs2251813	0.86[EUR][1000 genomes]
rs2253520	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2254423	0.86[EUR][1000 genomes]
rs2406933	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2854345	0.88[ASN][1000 genomes]
rs2854355	0.86[EUR][1000 genomes]
rs34217484	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs375105	0.81[EUR][1000 genomes]
rs3803188	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809328	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3818455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4151450	0.90[CEU][hapmap]
rs4151520	0.81[ASN][1000 genomes]
rs4594153	0.84[EUR][1000 genomes]
rs4600372	0.81[EUR][1000 genomes]
rs520342	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61973349	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7358982	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7984554	0.86[EUR][1000 genomes]
rs7984795	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs7999447	0.87[EUR][1000 genomes]
rs8001315	0.86[EUR][1000 genomes]
rs9316369	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526465	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs9526466	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526470	0.89[EUR][1000 genomes]
rs9534998	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535000	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535002	0.86[EUR][1000 genomes]
rs9535003	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535006	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535007	0.84[EUR][1000 genomes]
rs9535009	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535011	0.87[EUR][1000 genomes]
rs9562815	0.86[AFR][1000 genomes]
rs9568025	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9568026	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568027	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568028	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9568029	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs9568032	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568033	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568034	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568035	0.84[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.89[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	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9316367	LPAR6	cis	parietal	SCAN
rs9316367	ITM2B	cis	lymphoblastoid	seeQTL
rs9316367	C13orf1	cis	cerebellum	SCAN
rs9316367	ATAD2	trans	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48806600-48811000	Active TSS	Psoas Muscle	Psoas
2	chr13:48806600-48811000	Active TSS	Right Ventricle	heart
3	chr13:48806600-48812200	Active TSS	Ovary	ovary
4	chr13:48806600-48812200	Active TSS	Right Atrium	heart
5	chr13:48807000-48811200	Active TSS	Thymus	Thymus
6	chr13:48808200-48812000	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr13:48808400-48810800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr13:48808400-48810800	Weak transcription	Gastric	stomach
9	chr13:48808400-48810800	Weak transcription	Spleen	Spleen
10	chr13:48808400-48811800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr13:48808400-48815200	Weak transcription	Esophagus	oesophagus
12	chr13:48808400-48829000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr13:48808400-48829200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr13:48808400-48843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:48808600-48810800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr13:48808800-48811600	Flanking Active TSS	Osteobl	bone
17	chr13:48808800-48811800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr13:48808800-48812200	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr13:48809000-48811600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr13:48809000-48811600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr13:48809200-48811600	Transcr. at gene 5' and 3'	Dnd41	blood
22	chr13:48809200-48812200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr13:48809200-48812400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr13:48809400-48810800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr13:48809400-48811600	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
26	chr13:48809400-48811600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr13:48809400-48812200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr13:48809600-48812000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr13:48809600-48812000	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr13:48809600-48812200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr13:48809600-48812200	Enhancers	A549	lung
32	chr13:48809600-48837400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr13:48809800-48810800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr13:48809800-48811000	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr13:48809800-48811600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr13:48809800-48811600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
37	chr13:48809800-48811600	Enhancers	Small Intestine	intestine
38	chr13:48809800-48812400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
39	chr13:48809800-48812600	Flanking Active TSS	NHEK	skin
40	chr13:48809800-48829200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr13:48810000-48810800	Active TSS	Fetal Muscle Leg	muscle
42	chr13:48810000-48810800	Weak transcription	Left Ventricle	heart
43	chr13:48810000-48810800	Enhancers	Hela-S3	cervix
44	chr13:48810000-48810800	Enhancers	NHDF-Ad	bronchial
45	chr13:48810000-48811000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr13:48810000-48811000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr13:48810000-48811200	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr13:48810000-48811200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
49	chr13:48810000-48811400	Active TSS	Primary T cells fromperipheralblood	blood
50	chr13:48810000-48811600	Enhancers	H1 Cell Line	embryonic stem cell

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