Variant report

Variant	rs809415
Chromosome Location	chr3:99582242-99582243
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99562459..99564499-chr3:99581056..99583363,3	MCF-7	breast:
2	chr3:99574024..99577676-chr3:99581622..99586745,5	K562	blood:
3	chr3:99575233..99577676-chr3:99581601..99584216,3	K562	blood:
4	chr3:99579898..99582350-chr3:99587582..99589393,2	MCF-7	breast:

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

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];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1021102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[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]
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];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10936005	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936008	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[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];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13064704	0.91[JPT][hapmap]
rs13317017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
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	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1688782	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17174947	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718244	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1718245	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[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];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452321	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[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];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[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];0.90[AFR][1000 genomes];0.95[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];0.90[AFR][1000 genomes];0.97[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];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62283523	0.88[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];0.90[AFR][1000 genomes];0.97[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];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6790877	0.90[JPT][hapmap]
rs6799379	0.91[JPT][hapmap]
rs6802422	0.91[JPT][hapmap]
rs6803204	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6806178	0.91[JPT][hapmap]
rs6807176	0.91[JPT][hapmap]
rs68092024	0.85[AFR][1000 genomes]
rs6809988	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];0.96[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	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs704579	0.96[AMR][1000 genomes];0.91[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];0.81[AFR][1000 genomes];0.98[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];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609729	0.90[JPT][hapmap]
rs7610486	0.91[JPT][hapmap]
rs7616988	0.82[JPT][hapmap]
rs7629426	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[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];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638900	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[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];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793442	0.95[AMR][1000 genomes];0.96[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793447	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793448	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793449	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793452	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793453	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793455	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793458	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793459	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793460	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]
rs793461	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]
rs793462	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];0.97[ASN][1000 genomes]
rs793463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[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];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[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];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[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];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793470	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793471	0.88[AFR][1000 genomes];1.00[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];0.98[AMR][1000 genomes];0.92[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];0.94[AMR][1000 genomes];0.87[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];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793503	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[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];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs796978	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs812657	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];0.94[ASN][1000 genomes]
rs923470	0.91[JPT][hapmap]
rs923471	0.91[JPT][hapmap]
rs9817005	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9833888	0.91[JPT][hapmap]
rs9833980	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];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[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
rs809415	FILIP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99563200-99593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:99565200-99585000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:99565600-99584800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:99565600-99589400	Weak transcription	K562	blood
7	chr3:99569000-99589600	Weak transcription	Colonic Mucosa	Colon
8	chr3:99573200-99594000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:99573400-99589200	Genic enhancers	HepG2	liver
10	chr3:99573600-99584800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:99574000-99584000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:99574400-99590000	Weak transcription	Liver	Liver
13	chr3:99575000-99587000	Weak transcription	Pancreas	Pancrea
14	chr3:99575000-99593600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:99575200-99587000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:99576000-99587600	Genic enhancers	NHDF-Ad	bronchial
17	chr3:99576400-99585000	Weak transcription	A549	lung
18	chr3:99577400-99587200	Weak transcription	Brain Anterior Caudate	brain
19	chr3:99578200-99582600	Genic enhancers	NHLF	lung
20	chr3:99578200-99585400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:99578800-99584400	Strong transcription	Fetal Intestine Large	intestine
22	chr3:99579200-99582400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:99579200-99582400	Genic enhancers	Aorta	Aorta
24	chr3:99579200-99582400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr3:99579200-99591000	Genic enhancers	NH-A	brain
26	chr3:99579400-99583000	Weak transcription	Stomach Mucosa	stomach
27	chr3:99579400-99587000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:99579400-99591000	Weak transcription	Fetal Lung	lung
29	chr3:99579600-99582400	Strong transcription	NHEK	skin
30	chr3:99579600-99584000	Weak transcription	HMEC	breast
31	chr3:99579600-99585200	Weak transcription	Small Intestine	intestine
32	chr3:99579600-99585400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:99579600-99592400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:99580000-99582600	Strong transcription	Placenta	Placenta
35	chr3:99580400-99585200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:99580400-99585200	Weak transcription	Fetal Kidney	kidney
37	chr3:99580400-99585400	Strong transcription	Fetal Muscle Leg	muscle
38	chr3:99580600-99582400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:99580600-99582600	Strong transcription	Fetal Stomach	stomach
40	chr3:99580600-99585200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:99580600-99587000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:99580600-99587600	Weak transcription	Brain Angular Gyrus	brain
43	chr3:99580800-99590800	Weak transcription	Lung	lung
44	chr3:99581200-99589200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:99581400-99583600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:99581400-99585400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:99581400-99585400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:99581400-99594000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr3:99581600-99582800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:99581600-99583000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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