Variant report

Variant	rs11139997
Chromosome Location	chr9:72338610-72338611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
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[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10867952	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10867966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10867987	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10868033	1.00[CEU][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10868041	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11140181	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11140185	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140189	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140204	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140205	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140206	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140208	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11791457	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11792104	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11793130	0.84[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12376529	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13287102	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]
rs13293591	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13293770	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1411411	0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1536993	0.86[GIH][hapmap]
rs2026795	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];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56040923	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs918337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11139997	PTAR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72323600-72344400	Weak transcription	NHEK	skin
2	chr9:72323600-72360800	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:72323800-72357600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr9:72324200-72361000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:72324600-72359800	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr9:72324800-72345200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:72325000-72340400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:72325000-72358800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:72325400-72346200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr9:72326000-72339800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:72326000-72345000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:72326600-72344600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:72326600-72346400	Weak transcription	Small Intestine	intestine
14	chr9:72327800-72366800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:72328000-72345000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:72328600-72341000	Strong transcription	Fetal Thymus	thymus
17	chr9:72329000-72344400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr9:72329400-72338800	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr9:72329400-72339600	Strong transcription	Primary T cells from cord blood	blood
20	chr9:72329600-72345000	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:72330000-72349600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:72330200-72339600	Strong transcription	Primary B cells from cord blood	blood
23	chr9:72330200-72339800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:72330600-72346200	Weak transcription	Colonic Mucosa	Colon
25	chr9:72330600-72357400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr9:72330800-72341000	Strong transcription	Dnd41	blood
27	chr9:72331200-72346600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:72332200-72344600	Weak transcription	Hela-S3	cervix
29	chr9:72332600-72339000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:72332600-72339800	Strong transcription	Fetal Muscle Leg	muscle
31	chr9:72332800-72339000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:72333400-72374000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:72333600-72342000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr9:72333600-72344600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr9:72333600-72344600	Weak transcription	Brain Substantia Nigra	brain
36	chr9:72333600-72345000	Weak transcription	Aorta	Aorta
37	chr9:72333600-72345000	Weak transcription	Esophagus	oesophagus
38	chr9:72333600-72345000	Weak transcription	Fetal Stomach	stomach
39	chr9:72333600-72345000	Weak transcription	Right Ventricle	heart
40	chr9:72333600-72345200	Weak transcription	Lung	lung
41	chr9:72333600-72345400	Weak transcription	NHLF	lung
42	chr9:72333800-72344400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr9:72333800-72345000	Weak transcription	Ovary	ovary
44	chr9:72334400-72338800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr9:72334600-72340800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr9:72334800-72339600	Strong transcription	Adipose Nuclei	Adipose
47	chr9:72334800-72340000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:72335000-72339600	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr9:72335000-72339800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr9:72335200-72338800	Strong transcription	A549	lung

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