Variant report

Variant	rs1147709
Chromosome Location	chr3:120171720-120171721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr3:120171699-120171764	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120166952..120169851-chr3:120171116..120172868,2	MCF-7	breast:

Variant related genes	Relation type
FSTL1	TF binding region
ENSG00000163430	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	0.89[CHB][hapmap];0.81[LWK][hapmap]
rs1147706	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1147710	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147712	0.84[ASN][1000 genomes]
rs1147714	0.84[ASN][1000 genomes]
rs1147715	0.84[ASN][1000 genomes]
rs1147716	0.84[ASN][1000 genomes]
rs1147718	0.80[ASN][1000 genomes]
rs1259309	0.84[ASN][1000 genomes]
rs1259311	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1259312	0.84[ASN][1000 genomes]
rs1259329	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1259331	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1259332	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1259334	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1259336	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1259337	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1259338	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1259339	0.83[CHB][hapmap]
rs1259456	0.84[ASN][1000 genomes]
rs1259471	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259472	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259473	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1262395	0.84[ASN][1000 genomes]
rs1267675	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1267693	0.82[ASN][1000 genomes]
rs1270209	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1520881	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1716835	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1716837	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1733296	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1733298	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1733299	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1733301	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1733303	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1733304	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1733306	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1733307	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1733319	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2252084	0.83[CHB][hapmap]
rs2700262	0.84[ASN][1000 genomes]
rs2702155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5000757	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768839	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs735138	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs874477	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[EUR][1000 genomes]
rs874478	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs874479	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]
rs874480	0.95[EUR][1000 genomes]
rs9631455	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs988924	0.83[CHB][hapmap];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
rs1147709	FSTL1	cis	parietal	SCAN
rs1147709	FSTL1	cis	cerebellum	SCAN
rs1147709	NR1I2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120170400-120171800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr3:120170400-120190800	Weak transcription	Aorta	Aorta
3	chr3:120170600-120171800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:120170600-120171800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:120170600-120173000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:120170600-120178000	Weak transcription	Left Ventricle	heart
7	chr3:120170600-120178800	Weak transcription	Brain Germinal Matrix	brain
8	chr3:120170800-120171800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:120170800-120172000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:120170800-120172000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:120170800-120173000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:120170800-120178200	Weak transcription	Right Atrium	heart
13	chr3:120171000-120171800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr3:120171000-120171800	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr3:120171000-120171800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:120171000-120172000	Enhancers	H9 Cell Line	embryonic stem cell
17	chr3:120171000-120172000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
18	chr3:120171000-120172600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:120171000-120172800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:120171000-120179600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:120171200-120172200	Enhancers	Hela-S3	cervix
22	chr3:120171400-120171800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:120171400-120172000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:120171400-120179400	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:120171600-120172000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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