Variant report

Variant	rs793460
Chromosome Location	chr3:99615733-99615734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99614799..99616981-chr3:99982145..99984761,2	K562	blood:
2	chr3:99614799..99617137-chr3:99982145..99984761,3	K562	blood:
3	chr3:99593619..99595201-chr3:99613248..99616084,2	K562	blood:
4	chr3:99613503..99616492-chr3:99619175..99621373,2	K562	blood:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10049383	0.91[JPT][hapmap]
rs1016914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1017968	0.89[JPT][hapmap]
rs1021102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1021103	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs10212525	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs1021341	0.91[JPT][hapmap]
rs1038294	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs10511177	0.91[JPT][hapmap]
rs1059905	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1087198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10936005	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936008	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1287283	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13064704	0.91[JPT][hapmap]
rs13069311	0.91[JPT][hapmap]
rs13317017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13323143	0.91[JPT][hapmap]
rs1489816	0.82[JPT][hapmap]
rs1688766	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs1688771	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs1688774	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1688782	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17174947	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718244	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1718245	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1857290	0.82[YRI][hapmap]
rs2452320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452321	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075038	0.91[JPT][hapmap];0.89[YRI][hapmap]
rs4244711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244713	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4361315	0.91[JPT][hapmap]
rs4479633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4571265	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4928232	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62283523	0.86[AMR][1000 genomes]
rs629120	0.89[YRI][hapmap]
rs6440938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651511	0.82[YRI][hapmap]
rs668668	0.82[YRI][hapmap]
rs6765027	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6790535	0.91[JPT][hapmap]
rs6790877	0.90[JPT][hapmap]
rs6799379	0.91[JPT][hapmap]
rs6802422	0.91[JPT][hapmap]
rs6803204	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6806178	0.91[JPT][hapmap]
rs6807176	0.91[JPT][hapmap]
rs68092024	0.90[AFR][1000 genomes]
rs6809988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694429	0.89[YRI][hapmap]
rs704570	0.91[JPT][hapmap];0.90[YRI][hapmap]
rs704573	0.91[JPT][hapmap]
rs704575	0.83[JPT][hapmap]
rs704578	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs704579	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs704581	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs704582	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs704583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609729	0.90[JPT][hapmap]
rs7610486	0.91[JPT][hapmap]
rs7616988	0.82[JPT][hapmap]
rs7620228	0.91[JPT][hapmap]
rs7627991	0.91[JPT][hapmap]
rs7629426	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638900	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792834	0.82[JPT][hapmap];0.89[YRI][hapmap]
rs792840	0.82[JPT][hapmap]
rs792841	0.82[JPT][hapmap]
rs793440	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793442	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793445	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793448	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793449	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793452	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793453	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793455	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793458	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793459	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793470	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793471	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs793474	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793479	0.81[JPT][hapmap]
rs793492	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793494	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs793495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs793496	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793499	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs793501	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793503	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs796978	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs809415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs812657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs923470	0.91[JPT][hapmap]
rs923471	0.91[JPT][hapmap]
rs9814359	0.91[JPT][hapmap]
rs9815439	0.90[JPT][hapmap]
rs9817005	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9823908	0.91[JPT][hapmap]
rs9828079	0.91[JPT][hapmap]
rs9833888	0.91[JPT][hapmap]
rs9833980	0.91[JPT][hapmap]
rs9841186	0.91[JPT][hapmap]
rs9851645	0.91[JPT][hapmap]
rs9864437	0.91[JPT][hapmap]
rs9872871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873709	0.91[JPT][hapmap]
rs9873878	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs9875640	0.91[JPT][hapmap]

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	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
2	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs793460	FILIP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99600800-99638600	Weak transcription	Left Ventricle	heart
2	chr3:99604600-99648200	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99613000-99616000	Enhancers	Primary B cells from cord blood	blood
4	chr3:99613400-99616400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:99613600-99616000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:99613800-99615800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:99613800-99615800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr3:99613800-99616000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:99614200-99615800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:99614200-99615800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr3:99614200-99615800	Enhancers	Osteobl	bone
12	chr3:99614200-99616000	Enhancers	HMEC	breast
13	chr3:99614200-99616200	Enhancers	Brain Germinal Matrix	brain
14	chr3:99614400-99615800	Enhancers	Hela-S3	cervix
15	chr3:99614400-99616200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:99614400-99616600	Enhancers	HepG2	liver
17	chr3:99614600-99615800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:99614600-99615800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:99614600-99616000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:99614600-99616000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:99614600-99616000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr3:99614800-99615800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:99614800-99619400	Weak transcription	Psoas Muscle	Psoas
24	chr3:99615000-99615800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:99615000-99619400	Weak transcription	Fetal Lung	lung
26	chr3:99615200-99615800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr3:99615200-99615800	Enhancers	NH-A	brain
28	chr3:99615200-99619400	Weak transcription	Brain Angular Gyrus	brain
29	chr3:99615200-99620600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:99615400-99615800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr3:99615400-99615800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:99615400-99615800	Enhancers	NHEK	skin
33	chr3:99615400-99616000	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr3:99615400-99616000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:99615400-99616000	Enhancers	HUVEC	blood vessel
36	chr3:99615400-99617000	Weak transcription	NHLF	lung
37	chr3:99615400-99618400	Weak transcription	Adipose Nuclei	Adipose
38	chr3:99615400-99618600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:99615400-99619600	Weak transcription	Stomach Mucosa	stomach
40	chr3:99615400-99619600	Weak transcription	HSMMtube	muscle
41	chr3:99615400-99619800	Weak transcription	Fetal Stomach	stomach
42	chr3:99615400-99619800	Enhancers	NHDF-Ad	bronchial
43	chr3:99615400-99620200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:99615600-99615800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr3:99615600-99616000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:99615600-99616000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:99615600-99616400	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr3:99615600-99616400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:99615600-99617600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:99615600-99617800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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