Variant report

Variant	rs704581
Chromosome Location	chr3:99556160-99556161
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99554227..99558191-chr3:100053593..100055685,3	MCF-7	breast:
2	chr3:99550448..99553983-chr3:99555200..99558559,3	K562	blood:

Variant related genes	Relation type
ENSG00000114021	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10049383	0.81[JPT][hapmap]
rs1016914	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1021102	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1021103	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs10212525	0.81[JPT][hapmap];0.82[YRI][hapmap]
rs1038294	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs10511177	0.81[JPT][hapmap]
rs1059905	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1087198	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10936005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936008	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1287283	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13317017	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1688766	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1688771	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs1688774	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1688782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17174947	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1718244	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1718245	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2452320	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2452321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4075038	0.81[JPT][hapmap]
rs4244711	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4244713	0.95[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4361315	0.81[JPT][hapmap];0.91[YRI][hapmap]
rs4479633	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4571265	0.81[JPT][hapmap];0.82[YRI][hapmap]
rs4928232	0.95[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62283523	0.86[AMR][1000 genomes]
rs6440938	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6765027	0.95[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6803204	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6809988	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs704570	0.81[JPT][hapmap]
rs704573	0.81[JPT][hapmap]
rs704578	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs704579	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs704582	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs704583	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7610486	0.81[JPT][hapmap]
rs7616988	0.91[YRI][hapmap]
rs7629426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636447	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]
rs7638900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793442	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793445	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793447	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793448	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793449	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793455	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793458	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793459	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793460	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]
rs793461	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]
rs793462	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];0.94[ASN][1000 genomes]
rs793463	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs793465	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793466	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];0.94[ASN][1000 genomes]
rs793467	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793468	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793470	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793471	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793492	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs793494	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793495	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793496	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs793499	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs793501	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs796977	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs809415	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]
rs812657	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9817005	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9833888	0.81[JPT][hapmap]
rs9872871	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9873709	0.81[JPT][hapmap];0.91[YRI][hapmap]
rs9873878	0.81[JPT][hapmap];0.82[YRI][hapmap]
rs9875640	0.81[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
rs704581	FILIP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99562600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
3	chr3:99537800-99561800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:99537800-99562400	Weak transcription	Left Ventricle	heart
5	chr3:99538000-99556800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:99538000-99563600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
8	chr3:99543000-99557200	Weak transcription	Psoas Muscle	Psoas
9	chr3:99543000-99562600	Weak transcription	Placenta	Placenta
10	chr3:99544200-99561800	Weak transcription	NHLF	lung
11	chr3:99544200-99564800	Weak transcription	K562	blood
12	chr3:99544400-99557800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:99544400-99561800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:99544400-99561800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:99544800-99558000	Weak transcription	NHEK	skin
16	chr3:99545000-99557800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:99545000-99558000	Weak transcription	HMEC	breast
18	chr3:99545000-99562000	Weak transcription	HSMM	muscle
19	chr3:99549400-99556800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:99551000-99561800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:99551200-99560200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:99551200-99566000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:99551600-99562600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr3:99552400-99561600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:99552600-99556600	Weak transcription	Fetal Intestine Small	intestine
26	chr3:99552800-99557200	Weak transcription	Right Atrium	heart
27	chr3:99552800-99558200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:99552800-99561600	Weak transcription	Fetal Stomach	stomach
29	chr3:99552800-99561600	Weak transcription	Osteobl	bone
30	chr3:99552800-99561800	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:99552800-99562000	Weak transcription	Adipose Nuclei	Adipose
32	chr3:99552800-99562400	Weak transcription	Pancreas	Pancrea
33	chr3:99553000-99561800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:99553400-99557000	Weak transcription	Aorta	Aorta
35	chr3:99554000-99562400	Weak transcription	GM12878-XiMat	blood
36	chr3:99554400-99557200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr3:99554600-99556400	Enhancers	HUVEC	blood vessel
38	chr3:99554800-99558200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:99554800-99561600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:99554800-99561800	Weak transcription	Hela-S3	cervix
41	chr3:99555400-99557000	Enhancers	Small Intestine	intestine
42	chr3:99555800-99558000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:99555800-99562000	Weak transcription	Ovary	ovary
44	chr3:99556000-99556200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:99556000-99556200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr3:99556000-99556600	Enhancers	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links