Variant report

Variant	rs787209
Chromosome Location	chr3:120040449-120040450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120032416..120034924-chr3:120037587..120040555,3	MCF-7	breast:
2	chr3:120040040..120041629-chr3:120046647..120048331,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1009248	0.84[ASN][1000 genomes]
rs10511400	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.88[ASN][1000 genomes]
rs1085615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147700	0.83[YRI][hapmap]
rs11554681	0.84[LWK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs11708686	0.83[YRI][hapmap]
rs12495760	0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13075278	0.82[LWK][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs13075658	0.84[AFR][1000 genomes]
rs13100050	0.82[LWK][hapmap];0.89[YRI][hapmap]
rs13314898	0.88[EUR][1000 genomes]
rs1515575	0.92[YRI][hapmap]
rs16831033	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16831036	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2176093	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2319674	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2943757	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2971211	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs34104182	0.88[ASN][1000 genomes]
rs3914498	0.89[YRI][hapmap]
rs4676695	0.84[AFR][1000 genomes]
rs57086352	0.80[ASN][1000 genomes]
rs58556686	0.96[ASN][1000 genomes]
rs6438577	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6771381	0.80[ASN][1000 genomes]
rs6782419	0.84[ASN][1000 genomes]
rs6791815	0.80[ASN][1000 genomes]
rs6803206	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6803428	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6806659	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs701988	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72956869	0.80[ASN][1000 genomes]
rs72956871	0.84[ASN][1000 genomes]
rs7632516	0.96[ASN][1000 genomes]
rs787188	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs787191	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs787195	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787198	1.00[CEU][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs9817398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9822269	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9822672	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9874631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs787209	FSTL1	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120024400-120049200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:120025400-120040600	Weak transcription	Fetal Lung	lung
3	chr3:120026600-120042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:120026600-120060800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:120026800-120049200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:120026800-120067200	Weak transcription	Aorta	Aorta
7	chr3:120030000-120042600	Weak transcription	HMEC	breast
8	chr3:120031000-120041200	Weak transcription	Fetal Stomach	stomach
9	chr3:120031000-120042400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:120031000-120055600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:120031400-120040600	Weak transcription	Ovary	ovary
12	chr3:120031400-120042400	Weak transcription	A549	lung
13	chr3:120032400-120047600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:120032800-120042400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:120033000-120042200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:120033000-120042800	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:120033200-120044400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:120033200-120050000	Weak transcription	Spleen	Spleen
19	chr3:120033200-120060400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:120033200-120060400	Weak transcription	Pancreas	Pancrea
21	chr3:120033200-120067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:120033600-120041000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:120034600-120052400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:120035200-120049800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:120035800-120043000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:120036400-120041600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:120036600-120053600	Weak transcription	Fetal Heart	heart
28	chr3:120037200-120052200	Weak transcription	Brain Anterior Caudate	brain
29	chr3:120037600-120042600	Weak transcription	NHDF-Ad	bronchial
30	chr3:120038200-120041600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr3:120038200-120049200	Weak transcription	Fetal Kidney	kidney
32	chr3:120038400-120040600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:120038400-120041600	Weak transcription	Brain Germinal Matrix	brain
34	chr3:120038400-120046600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:120038600-120040800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:120038600-120041000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:120038600-120041600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:120038600-120042600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:120038600-120049200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr3:120038800-120040600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:120038800-120040600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:120038800-120040600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:120038800-120041200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:120038800-120041400	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:120038800-120042600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:120038800-120049000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:120038800-120049800	Weak transcription	Fetal Brain Female	brain
48	chr3:120038800-120051600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr3:120039000-120041200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr3:120039000-120041200	Weak transcription	Fetal Intestine Small	intestine

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