Variant report

Variant	rs13287102
Chromosome Location	chr9:72362026-72362027
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:72359106..72363474-chr9:72372322..72376083,7	MCF-7	breast:
2	chr9:72361031..72363861-chr9:72374055..72376198,2	MCF-7	breast:
3	chr9:72361796..72363677-chr9:72418688..72421431,2	K562	blood:
4	chr9:72360748..72362784-chr9:72371625..72375303,3	K562	blood:
5	chr9:72360152..72362800-chr9:72364655..72369107,4	K562	blood:
6	chr9:72360551..72362642-chr9:72371189..72374048,2	K562	blood:
7	chr9:72360858..72363722-chr9:72367124..72369107,2	K562	blood:

Variant related genes	Relation type
ENSG00000188647	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10780598	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10867952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10867966	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10867987	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868041	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11139997	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140181	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11140185	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140189	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140204	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140205	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140206	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140208	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791457	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11792104	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793130	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12376529	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13293591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13293770	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1411411	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536993	0.86[GIH][hapmap]
rs2026795	0.84[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56040923	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs918337	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471309	chr9:72273898-72410323	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1048622	chr9:72303617-72371795	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1050920	chr9:72345297-72579301	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking 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	18 gene(s)	inside rSNPs	diseases
4	nsv831611	chr9:72361905-72512134	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13287102	PTAR1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72327800-72366800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:72333400-72374000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:72337400-72366400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:72347000-72364600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr9:72347200-72364800	Weak transcription	Fetal Brain Female	brain
6	chr9:72347200-72371400	Weak transcription	Small Intestine	intestine
7	chr9:72347200-72373400	Weak transcription	Esophagus	oesophagus
8	chr9:72347200-72373400	Weak transcription	Fetal Intestine Small	intestine
9	chr9:72347200-72374200	Weak transcription	Spleen	Spleen
10	chr9:72347400-72362200	Weak transcription	Aorta	Aorta
11	chr9:72347400-72374000	Weak transcription	Gastric	stomach
12	chr9:72347600-72362200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:72347600-72362600	Weak transcription	Right Ventricle	heart
14	chr9:72347600-72368400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr9:72348400-72363800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:72348600-72364000	Weak transcription	Colonic Mucosa	Colon
17	chr9:72348800-72362200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:72348800-72362200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr9:72348800-72362400	Weak transcription	Lung	lung
20	chr9:72348800-72368600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr9:72348800-72373000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr9:72348800-72373000	Weak transcription	NHEK	skin
23	chr9:72348800-72373200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:72349000-72362200	Weak transcription	Brain Angular Gyrus	brain
25	chr9:72349200-72363800	Weak transcription	NH-A	brain
26	chr9:72349600-72363800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:72350200-72363800	Weak transcription	HSMMtube	muscle
28	chr9:72352400-72362200	Weak transcription	Fetal Stomach	stomach
29	chr9:72352400-72365800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr9:72353400-72365800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:72353600-72362200	Weak transcription	Psoas Muscle	Psoas
32	chr9:72356600-72364000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:72356800-72370000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr9:72358600-72363000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:72359000-72362800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:72359400-72362200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr9:72359600-72362400	Genic enhancers	Primary T cells from cord blood	blood
38	chr9:72359600-72363200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:72359600-72363400	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr9:72359600-72363800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:72359600-72365600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr9:72359600-72365600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:72359600-72365800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
44	chr9:72359800-72362400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
45	chr9:72359800-72365800	Strong transcription	Dnd41	blood
46	chr9:72359800-72373400	Weak transcription	Placenta	Placenta
47	chr9:72360000-72363200	Weak transcription	Osteobl	bone
48	chr9:72360000-72371400	Weak transcription	Pancreas	Pancrea
49	chr9:72360200-72362600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
50	chr9:72360200-72372200	Weak transcription	HMEC	breast

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