Variant report

Variant	rs9288129
Chromosome Location	chr2:187302876-187302877
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10169008	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10169206	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10177153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10190003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196955	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198525	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200749	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10205170	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10208643	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497671	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931240	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11675633	0.89[ASN][1000 genomes]
rs11688988	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690758	0.89[ASN][1000 genomes]
rs11692347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11888880	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11888881	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11901465	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11903027	0.89[ASN][1000 genomes]
rs12328822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13397188	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398352	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13401304	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13414850	0.89[ASN][1000 genomes]
rs13428033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1448848	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1448849	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs1448855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1448857	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16827968	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1868383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2084488	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2084489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084490	0.84[ASN][1000 genomes]
rs2197139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2370688	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2887826	0.89[ASN][1000 genomes]
rs34234405	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35642346	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56137171	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61434493	0.89[ASN][1000 genomes]
rs6434174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6709401	1.00[CHB][hapmap]
rs6710436	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6715493	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717505	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717525	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6721789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728382	0.89[ASN][1000 genomes]
rs6728400	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6731567	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6744717	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs72895449	0.89[ASN][1000 genomes]
rs7579259	0.89[ASN][1000 genomes]
rs7582412	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7584137	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7585905	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7597954	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606920	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9917285	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868949	chr2:186657142-187327560	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv428067	chr2:187171324-187334779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1005680	chr2:187244500-187320653	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv536080	chr2:187244500-187320653	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1001927	chr2:187264940-187325667	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv997835	chr2:187265730-187327561	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv536081	chr2:187265730-187327561	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9288129	PNPLA7	trans	brain	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187290600-187304200	Weak transcription	Stomach Mucosa	stomach
2	chr2:187293000-187304400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr2:187293800-187322000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:187297200-187303200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:187297600-187305200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:187297800-187331200	Weak transcription	Left Ventricle	heart
7	chr2:187298200-187304400	Weak transcription	Pancreas	Pancrea
8	chr2:187299600-187319600	Weak transcription	Adipose Nuclei	Adipose
9	chr2:187299600-187322800	Weak transcription	Aorta	Aorta
10	chr2:187299800-187305200	Weak transcription	Liver	Liver
11	chr2:187299800-187305600	Weak transcription	Spleen	Spleen
12	chr2:187300200-187305400	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr2:187300400-187303600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:187301000-187303400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:187301000-187303400	Weak transcription	Right Atrium	heart
16	chr2:187301200-187316000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:187301400-187303000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:187301400-187304200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:187301400-187321000	Weak transcription	Primary T cells from cord blood	blood
20	chr2:187301400-187322600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:187301600-187303200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:187301600-187315200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:187301600-187322600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:187301800-187304400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:187301800-187315600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:187302200-187319600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:187302200-187323200	Weak transcription	Ovary	ovary
28	chr2:187302400-187303200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr2:187302600-187321200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:187302800-187303800	ZNF genes & repeats	Primary B cells from cord blood	blood
31	chr2:187302800-187308600	Weak transcription	Duodenum Mucosa	Duodenum

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