Variant report

Variant	rs793501
Chromosome Location	chr3:99591638-99591639
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99591437..99593701-chr3:99599542..99601612,3	K562	blood:
2	chr3:99582314..99585905-chr3:99590964..99594499,4	MCF-7	breast:
3	chr3:99589147..99593753-chr3:99593896..99597054,6	MCF-7	breast:
4	chr3:99589828..99592269-chr3:99639312..99642221,3	K562	blood:
5	chr3:99589389..99592521-chr3:99720573..99723632,4	MCF-7	breast:
6	chr3:99584236..99588094-chr3:99589040..99591682,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1016914	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1021102	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1059905	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1087198	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10936005	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936008	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1287283	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13317017	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1688774	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1688782	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17174947	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718244	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1718245	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2452320	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452321	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244711	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244713	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4479633	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928232	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62283523	0.88[AMR][1000 genomes]
rs6440938	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765027	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6803204	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68092024	0.86[AFR][1000 genomes]
rs6809988	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
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	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs704583	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629426	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636447	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638900	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793440	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	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793447	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793448	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793449	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793452	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793453	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	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793459	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793460	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793461	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793462	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793463	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793465	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793466	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793467	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793468	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793470	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793471	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs793474	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793494	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs793495	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs793503	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796977	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs796978	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs809415	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs812657	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9817005	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9872871	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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
rs793501	FILIP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99563200-99593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:99573200-99594000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:99575000-99593600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:99579600-99592400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:99581400-99594000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:99583600-99593600	Weak transcription	Primary B cells from cord blood	blood
8	chr3:99585600-99592400	Enhancers	Fetal Kidney	kidney
9	chr3:99586200-99594000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:99587400-99592800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:99587400-99594600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:99588800-99592200	Flanking Active TSS	Colon Smooth Muscle	Colon
13	chr3:99589000-99592000	Flanking Active TSS	Rectal Smooth Muscle	rectum
14	chr3:99589200-99592000	Transcr. at gene 5' and 3'	HepG2	liver
15	chr3:99589400-99593000	Enhancers	Placenta Amnion	Placenta Amnion
16	chr3:99589600-99592000	Enhancers	Gastric	stomach
17	chr3:99589800-99591800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:99590000-99595800	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr3:99590200-99592600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:99590200-99595800	Active TSS	Right Atrium	heart
21	chr3:99590200-99596000	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr3:99590400-99592400	Enhancers	A549	lung
23	chr3:99590400-99592600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:99590400-99592800	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr3:99590600-99592000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:99590600-99593600	Enhancers	Stomach Mucosa	stomach
27	chr3:99590600-99595800	Active TSS	Ovary	ovary
28	chr3:99590600-99596400	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr3:99590800-99591800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:99590800-99594200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:99591000-99592000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:99591000-99592600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:99591000-99592600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:99591000-99593000	Enhancers	HMEC	breast
35	chr3:99591000-99594000	Weak transcription	Liver	Liver
36	chr3:99591000-99594200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:99591200-99591800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:99591200-99591800	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr3:99591200-99591800	Enhancers	Small Intestine	intestine
40	chr3:99591200-99591800	Enhancers	NHEK	skin
41	chr3:99591200-99592000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:99591200-99592000	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr3:99591200-99592400	Weak transcription	Placenta	Placenta
44	chr3:99591200-99592600	Flanking Active TSS	NH-A	brain
45	chr3:99591200-99593400	Active TSS	Left Ventricle	heart
46	chr3:99591200-99594400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:99591200-99594400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:99591200-99594400	Weak transcription	Lung	lung
49	chr3:99591200-99594400	Weak transcription	Pancreas	Pancrea
50	chr3:99591200-99595600	Active TSS	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links