Variant report

Variant	rs17379739
Chromosome Location	chr3:99724792-99724793
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99723070..99725877-chr3:99978503..99980301,2	MCF-7	breast:
2	chr3:99719980..99722131-chr3:99722963..99725848,2	K562	blood:
3	chr3:99723727..99725718-chr3:99976911..99979235,2	K562	blood:
4	chr3:99593399..99595369-chr3:99721874..99725950,4	MCF-7	breast:
5	chr3:99720592..99723772-chr3:99724475..99727275,3	MCF-7	breast:
6	chr3:99601766..99603960-chr3:99724495..99726434,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction
ENSG00000036054	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10049383	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1017968	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10212525	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1021341	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10511177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13064704	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13069311	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13093838	0.81[EUR][1000 genomes]
rs13323143	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1489816	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17392948	0.81[EUR][1000 genomes]
rs17393059	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291494	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291495	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28503408	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28714363	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34922392	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34996634	0.81[EUR][1000 genomes]
rs35154249	0.81[EUR][1000 genomes]
rs35521705	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35669453	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35844878	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35885423	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4075038	0.81[EUR][1000 genomes]
rs4279135	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4571265	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928234	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62285461	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285462	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62285471	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62285473	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62285478	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6790535	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6790877	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6799379	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6802422	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6806178	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6807176	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71313585	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610486	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616988	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7620228	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7627991	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs923470	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs923471	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9810235	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814359	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9815439	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9823908	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9828079	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9832186	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833888	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833980	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9834484	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9837602	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9841186	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9851645	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9852435	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9853823	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864437	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9873709	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873878	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875640	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875664	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878931	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17379739	FILIP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99716400-99758800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:99720200-99727600	Enhancers	Stomach Mucosa	stomach
4	chr3:99720800-99724800	Weak transcription	Psoas Muscle	Psoas
5	chr3:99720800-99725000	Enhancers	Fetal Intestine Small	intestine
6	chr3:99721400-99725000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr3:99721400-99729400	Enhancers	HUVEC	blood vessel
8	chr3:99722000-99725800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:99722000-99726200	Weak transcription	Fetal Stomach	stomach
10	chr3:99722000-99726400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:99722000-99726400	Weak transcription	Right Atrium	heart
12	chr3:99722200-99724800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:99722200-99724800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:99722200-99725600	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:99722200-99725600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:99722200-99726400	Weak transcription	K562	blood
17	chr3:99722400-99725200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:99722400-99727000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:99722400-99741400	Weak transcription	Aorta	Aorta
20	chr3:99722400-99751000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:99722600-99724800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:99722600-99725200	Weak transcription	NHLF	lung
23	chr3:99722600-99726400	Weak transcription	Fetal Heart	heart
24	chr3:99722600-99741200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:99723000-99724800	Weak transcription	Esophagus	oesophagus
26	chr3:99723200-99725000	Weak transcription	HepG2	liver
27	chr3:99723400-99725200	Enhancers	Small Intestine	intestine
28	chr3:99723400-99725800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:99723400-99725800	Enhancers	HSMMtube	muscle
30	chr3:99723600-99725800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:99723600-99726000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr3:99723600-99727000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:99723800-99725000	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr3:99723800-99727600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr3:99724000-99724800	Weak transcription	NHEK	skin
36	chr3:99724000-99726000	Enhancers	Osteobl	bone
37	chr3:99724000-99727200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:99724000-99727400	Enhancers	Hela-S3	cervix
39	chr3:99724000-99729000	Enhancers	Fetal Kidney	kidney
40	chr3:99724200-99725200	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr3:99724200-99726000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr3:99724200-99726000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr3:99724200-99726200	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr3:99724200-99726400	Enhancers	HSMM	muscle
45	chr3:99724200-99728400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:99724400-99725000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr3:99724400-99725200	Enhancers	Fetal Muscle Leg	muscle
48	chr3:99724400-99726000	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr3:99724400-99727600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:99724600-99724800	Enhancers	Fetal Lung	lung

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