Variant report

Variant	rs159709
Chromosome Location	chr12:29753962-29753963
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10400534	0.85[CHB][hapmap]
rs10400541	0.82[CHB][hapmap]
rs10771545	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs10771546	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs10771547	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs11050270	0.95[JPT][hapmap]
rs11050271	0.95[JPT][hapmap]
rs11050273	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs11050278	0.95[JPT][hapmap]
rs11050280	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs11050292	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11050293	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11050297	0.89[JPT][hapmap]
rs11050298	0.83[ASN][1000 genomes]
rs11050299	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs11050300	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs11050301	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs11050302	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs11050319	0.95[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs11611194	0.95[JPT][hapmap]
rs12368037	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12371221	0.90[JPT][hapmap]
rs12579805	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12581671	0.95[JPT][hapmap]
rs12819780	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1326758	0.81[CHB][hapmap]
rs1409616	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1409617	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs159696	0.81[CHB][hapmap]
rs159701	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs159703	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs159704	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs159705	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs159707	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs159708	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159714	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159715	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1988548	0.82[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs2113879	0.83[JPT][hapmap]
rs2113880	0.83[JPT][hapmap]
rs2182547	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288132	0.95[JPT][hapmap]
rs2288133	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs2350532	0.83[JPT][hapmap]
rs2478469	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2478470	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2553077	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2766605	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2766606	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299444	0.82[CHB][hapmap]
rs299445	0.82[CHB][hapmap]
rs299455	0.95[JPT][hapmap]
rs299459	0.95[JPT][hapmap]
rs299462	0.83[JPT][hapmap]
rs299463	0.85[JPT][hapmap]
rs299465	0.83[JPT][hapmap]
rs299466	0.83[JPT][hapmap]
rs299472	0.83[JPT][hapmap]
rs299475	0.84[JPT][hapmap]
rs4931201	0.95[JPT][hapmap]
rs7294502	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs7295284	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7301491	0.95[JPT][hapmap]
rs7310555	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs7310895	0.82[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs7314549	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs9300191	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs994172	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1053629	chr12:29680163-29826626	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1051913	chr12:29741676-29770807	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs159709	P2RX5	trans	lymphoblastoid	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29709800-29756200	Weak transcription	HMEC	breast
2	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:29731800-29769600	Weak transcription	Hela-S3	cervix
4	chr12:29736800-29762800	Weak transcription	Fetal Stomach	stomach
5	chr12:29737200-29761800	Weak transcription	Right Ventricle	heart
6	chr12:29737200-29762400	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:29737200-29762800	Weak transcription	Psoas Muscle	Psoas
8	chr12:29743200-29769800	Weak transcription	NHLF	lung
9	chr12:29744400-29790800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:29744600-29754200	Weak transcription	Brain Anterior Caudate	brain
11	chr12:29744600-29765400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:29744600-29791000	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:29744800-29764600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:29744800-29778200	Weak transcription	Ovary	ovary
15	chr12:29745200-29755000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:29745200-29762000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:29746200-29757200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:29746200-29762200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr12:29747000-29757800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:29747400-29756400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:29748600-29762600	Weak transcription	Spleen	Spleen
22	chr12:29750000-29762200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:29750400-29757000	Weak transcription	Aorta	Aorta
24	chr12:29750400-29762600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:29752400-29761600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:29752600-29754400	Strong transcription	Left Ventricle	heart
27	chr12:29752600-29759800	Weak transcription	Adipose Nuclei	Adipose
28	chr12:29752600-29763000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr12:29752600-29763600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:29752600-29764600	Weak transcription	HSMMtube	muscle
31	chr12:29752600-29765600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:29752600-29768400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:29752600-29778200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:29752800-29755200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:29752800-29755400	Weak transcription	HSMM	muscle
36	chr12:29752800-29757000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:29752800-29759400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:29752800-29762400	Weak transcription	Liver	Liver
39	chr12:29753000-29757400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:29753400-29755200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:29753600-29755600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:29753600-29764800	Weak transcription	NHDF-Ad	bronchial
43	chr12:29753800-29755200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:29753800-29755800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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