Variant report

Variant	rs704573
Chromosome Location	chr3:99483271-99483272
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1016914	0.91[JPT][hapmap]
rs1021102	0.90[JPT][hapmap]
rs1021103	0.81[JPT][hapmap]
rs1038294	0.81[JPT][hapmap]
rs1087198	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs10936005	0.91[JPT][hapmap]
rs1287283	0.91[JPT][hapmap];0.82[MEX][hapmap]
rs13317017	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs1606481	0.93[CHB][hapmap]
rs1688766	0.81[JPT][hapmap]
rs1688771	0.81[JPT][hapmap]
rs1688782	0.91[JPT][hapmap]
rs1711557	0.93[CHB][hapmap]
rs1857290	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[TSI][hapmap]
rs2452320	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs2452321	0.91[JPT][hapmap]
rs4075038	0.81[JPT][hapmap]
rs4244711	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs4244713	0.90[JPT][hapmap];0.87[MEX][hapmap]
rs4479633	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs629120	0.93[CHB][hapmap]
rs6440938	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs651511	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs668668	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[TSI][hapmap]
rs6809988	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs694429	0.92[CHB][hapmap]
rs704570	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs704575	0.91[JPT][hapmap]
rs704581	0.81[JPT][hapmap]
rs704582	0.81[JPT][hapmap]
rs704583	0.91[JPT][hapmap];0.85[MEX][hapmap]
rs7629426	0.91[JPT][hapmap]
rs7636447	0.91[JPT][hapmap]
rs7638900	0.91[JPT][hapmap]
rs792828	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs792829	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes]
rs792832	0.89[JPT][hapmap]
rs792834	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs792839	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs792840	0.80[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs792841	0.80[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs793440	0.91[JPT][hapmap]
rs793445	0.91[JPT][hapmap]
rs793452	0.91[JPT][hapmap]
rs793453	0.91[JPT][hapmap]
rs793460	0.91[JPT][hapmap]
rs793461	0.91[JPT][hapmap]
rs793462	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs793463	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs793465	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs793466	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs793467	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs793468	0.91[JPT][hapmap];0.80[MEX][hapmap]
rs793470	0.91[JPT][hapmap]
rs793474	0.91[JPT][hapmap]
rs793479	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs793489	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs793490	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs793491	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs793492	0.81[JPT][hapmap]
rs793494	0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes]
rs793495	0.91[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes]
rs793496	0.81[JPT][hapmap]
rs793499	0.81[JPT][hapmap]
rs793503	0.91[JPT][hapmap]
rs796977	0.90[JPT][hapmap]
rs796978	0.91[JPT][hapmap]
rs809415	0.91[JPT][hapmap]
rs812657	0.91[JPT][hapmap];0.87[MEX][hapmap]
rs9872871	0.91[JPT][hapmap]

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	nsv877217	chr3:99418950-99496351	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv508231	chr3:99442020-99498951	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs704573	FILIP1L	Cis_1M	lymphoblastoid	RTeQTL
rs704573	FILIP1L	cis	parietal	SCAN
rs704573	SENP7	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99462400-99495600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:99472400-99484000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:99472400-99484000	Weak transcription	NHLF	lung
4	chr3:99472400-99493000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:99472400-99493000	Weak transcription	NHEK	skin
6	chr3:99472400-99493400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:99472600-99483800	Weak transcription	NH-A	brain
8	chr3:99474800-99486200	Weak transcription	NHDF-Ad	bronchial
9	chr3:99479200-99484000	Weak transcription	Aorta	Aorta
10	chr3:99480600-99484000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:99480600-99484000	Weak transcription	Right Ventricle	heart
12	chr3:99481600-99483400	Strong transcription	HUVEC	blood vessel
13	chr3:99482000-99483600	Weak transcription	HSMM	muscle
14	chr3:99482000-99484000	Weak transcription	HSMMtube	muscle
15	chr3:99482200-99483800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:99482400-99493000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:99482600-99486800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:99482800-99484000	Weak transcription	Adipose Nuclei	Adipose
19	chr3:99482800-99485200	Genic enhancers	Muscle Satellite Cultured Cells	--
20	chr3:99483000-99483600	Enhancers	Fetal Heart	heart
21	chr3:99483000-99485000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:99483000-99485000	Enhancers	Osteobl	bone
23	chr3:99483200-99484600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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