Variant report

Variant	rs874479
Chromosome Location	chr3:120158349-120158350
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:120158128..120161743-chr3:120167809..120171161,5	MCF-7	breast:
2	chr3:120136351..120139286-chr3:120156446..120159592,3	MCF-7	breast:
3	chr3:120066637..120068754-chr3:120157583..120159738,2	MCF-7	breast:
4	chr3:120155958..120158506-chr3:120167784..120170951,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163428	Chromatin interaction
ENSG00000163430	Chromatin interaction
ENSG00000240661	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1123897	0.94[CHB][hapmap];0.81[CHD][hapmap]
rs1147706	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1147709	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1147710	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1147712	0.81[ASN][1000 genomes]
rs1147714	0.81[ASN][1000 genomes]
rs1147715	0.81[ASN][1000 genomes]
rs1147716	0.81[ASN][1000 genomes]
rs1147720	0.83[CHB][hapmap]
rs1259309	0.81[ASN][1000 genomes]
rs1259311	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[EUR][1000 genomes]
rs1259312	0.81[ASN][1000 genomes]
rs1259318	0.83[CHB][hapmap]
rs1259329	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1259331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1259332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1259334	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1259336	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1259337	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1259338	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1259339	0.88[CHB][hapmap]
rs1259456	0.81[ASN][1000 genomes]
rs1259471	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259472	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259473	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1262395	0.81[ASN][1000 genomes]
rs1267675	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1270209	0.91[CEU][hapmap];0.83[CHB][hapmap];0.86[EUR][1000 genomes]
rs1520881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716835	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1716837	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1733296	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1733298	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1733299	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1733301	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1733303	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1733304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1733306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1733307	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1733319	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2252084	0.89[CHB][hapmap]
rs2700262	0.81[ASN][1000 genomes]
rs2702155	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5000757	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768839	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs735138	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs874477	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs874478	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874480	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9631455	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs988924	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	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
6	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
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs874479	FSTL1	cis	parietal	SCAN
rs874479	FSTL1	cis	cerebellum	SCAN
rs874479	NR1I2	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120137400-120162200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:120137800-120161600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:120138200-120162000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:120138200-120167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:120138200-120169200	Weak transcription	Gastric	stomach
6	chr3:120144400-120165800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:120145800-120168800	Weak transcription	Pancreas	Pancrea
8	chr3:120148000-120161000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:120149000-120161200	Genic enhancers	NHDF-Ad	bronchial
10	chr3:120151800-120166200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:120152000-120158400	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:120152600-120161400	Genic enhancers	Fetal Muscle Leg	muscle
13	chr3:120152600-120162200	Genic enhancers	Fetal Stomach	stomach
14	chr3:120153000-120167600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:120153200-120159400	Weak transcription	Spleen	Spleen
16	chr3:120153400-120160600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:120153800-120159400	Enhancers	Aorta	Aorta
18	chr3:120154000-120161200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr3:120154200-120159600	Genic enhancers	HSMM	muscle
20	chr3:120154400-120160400	Weak transcription	Brain Angular Gyrus	brain
21	chr3:120154800-120158400	Weak transcription	Fetal Intestine Small	intestine
22	chr3:120155200-120160200	Genic enhancers	HSMMtube	muscle
23	chr3:120155200-120163400	Genic enhancers	NHLF	lung
24	chr3:120155400-120159200	Weak transcription	HMEC	breast
25	chr3:120155400-120160800	Genic enhancers	Muscle Satellite Cultured Cells	--
26	chr3:120155400-120161400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:120155400-120162800	Enhancers	Right Atrium	heart
28	chr3:120155600-120160600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:120155800-120159200	Weak transcription	Brain Anterior Caudate	brain
30	chr3:120155800-120159200	Weak transcription	Esophagus	oesophagus
31	chr3:120155800-120168400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr3:120156000-120160600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:120156200-120166200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:120156400-120160000	Genic enhancers	Placenta Amnion	Placenta Amnion
35	chr3:120156400-120160800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:120156400-120160800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:120156600-120159200	Genic enhancers	Placenta	Placenta
38	chr3:120156600-120160000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:120156600-120160000	Genic enhancers	Left Ventricle	heart
40	chr3:120156600-120160800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:120156600-120161200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:120156600-120161400	Genic enhancers	Fetal Lung	lung
43	chr3:120156600-120168800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:120156800-120158400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:120156800-120160800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:120156800-120161000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr3:120156800-120165200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:120156800-120166000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr3:120157000-120158600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr3:120157000-120160200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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