Variant report

Variant	rs592055
Chromosome Location	chr10:96954479-96954480
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10128123	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10218877	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10509683	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10882566	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10882568	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11188223	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11188225	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11188228	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11188229	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11188230	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11572093	0.82[CHB][hapmap]
rs11598953	1.00[JPT][hapmap]
rs11872	1.00[JPT][hapmap]
rs12262878	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12764831	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs1341164	0.82[CHB][hapmap]
rs16872	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[YRI][hapmap]
rs17524438	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs1934955	0.82[CHB][hapmap]
rs1934957	0.82[CHB][hapmap]
rs1934982	0.82[CHB][hapmap]
rs1934983	0.82[CHB][hapmap]
rs2071426	0.85[CHB][hapmap]
rs2185571	0.82[CHB][hapmap]
rs2449809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs2478477	0.85[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs2478478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs2478479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs489807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs509736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs513661	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs585381	0.81[AMR][1000 genomes]
rs589801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs591157	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes]
rs591171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs592041	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs594448	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap]
rs604022	0.81[AMR][1000 genomes]
rs604373	0.81[AMR][1000 genomes]
rs610046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes]
rs610579	0.83[AMR][1000 genomes]
rs611343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs611416	0.81[AMR][1000 genomes]
rs612490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs613340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs614682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs616721	0.83[AMR][1000 genomes]
rs620196	0.81[AMR][1000 genomes]
rs626415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs627173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs628102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs633345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs634269	0.81[AMR][1000 genomes]
rs637465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs637724	0.81[AMR][1000 genomes]
rs637939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap]
rs641198	0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs646845	0.81[AMR][1000 genomes]
rs648638	0.81[AMR][1000 genomes]
rs648695	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap]
rs6583967	0.82[CHB][hapmap]
rs659949	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap]
rs664093	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap]
rs666786	0.81[AMR][1000 genomes]
rs669360	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs672428	0.81[AMR][1000 genomes]
rs672860	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs682477	0.80[AMR][1000 genomes]
rs685607	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs688706	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap]
rs689207	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap]
rs695217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7089303	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs7909072	1.00[JPT][hapmap]
rs815259	0.81[ASN][1000 genomes]
rs815266	0.81[AMR][1000 genomes]
rs815267	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs815268	0.81[AMR][1000 genomes]
rs815269	0.80[AMR][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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv21432	chr10:96856006-96996043	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1834151	chr10:96925446-96992955	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv825527	chr10:96954221-96954660	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
7	nsv820063	chr10:96954277-96954895	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs592055	PDLIM1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96943400-96955200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:96944000-96954800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr10:96944000-96955200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr10:96944000-96955800	Weak transcription	Aorta	Aorta
5	chr10:96944000-96961400	Weak transcription	Fetal Intestine Small	intestine
6	chr10:96944200-96990400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr10:96948600-96955200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:96949800-96980600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr10:96952800-96974600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:96953800-96954600	Enhancers	Fetal Muscle Leg	muscle
11	chr10:96953800-96954600	Flanking Active TSS	Fetal Thymus	thymus
12	chr10:96953800-96956200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr10:96953800-96956400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr10:96953800-96956800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr10:96953800-96956800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr10:96954000-96954600	Enhancers	Stomach Mucosa	stomach
17	chr10:96954000-96955800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr10:96954200-96954600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr10:96954200-96954600	Enhancers	Pancreas	Pancrea
20	chr10:96954200-96955400	Enhancers	HepG2	liver
21	chr10:96954400-96954600	Enhancers	HSMMtube	muscle
22	chr10:96954400-96954800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr10:96954400-96955800	Weak transcription	Thymus	Thymus
24	chr10:96954400-96956400	Enhancers	HUES64 Cell Line	embryonic stem cell

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