Variant report

Variant	rs11706480
Chromosome Location	chr3:141719380-141719381
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	STAT3	chr3:141719125-141719462	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr3:141719278-141719659	T-47D	breast:	n/a	n/a
3	FOS	chr3:141719263-141719382	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr3:141719142-141719462	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr3:141719139-141719397	MCF10A-Er-Src	breast:	n/a	n/a
6	EP300	chr3:141719242-141719624	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141713631..141715238-chr3:141716946..141719717,2	K562	blood:
2	chr3:141713631..141715353-chr3:141718217..141720483,2	K562	blood:

Variant related genes	Relation type
TFDP2	TF binding region
ENSG00000114126	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10935453	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11569198	0.83[CHB][hapmap]
rs11714792	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12496412	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13065446	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1355438	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1397764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1511299	0.99[ASN][1000 genomes]
rs1543064	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2063453	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs2063454	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs2271386	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs2861422	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2862125	0.95[ASN][1000 genomes]
rs34186890	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34392664	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35566385	0.90[EUR][1000 genomes]
rs3817176	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs4683653	0.80[CEU][hapmap];0.80[CHD][hapmap];0.92[TSI][hapmap]
rs4683658	0.95[ASN][1000 genomes]
rs6440057	0.97[ASN][1000 genomes]
rs6440060	0.92[ASN][1000 genomes]
rs6773343	0.88[JPT][hapmap]
rs6778085	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs6781340	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6791514	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6794342	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6795301	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs72990266	0.86[ASN][1000 genomes]
rs7619506	0.82[CHB][hapmap]
rs7630893	0.94[ASN][1000 genomes]
rs7642874	0.90[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs7644155	0.95[ASN][1000 genomes]
rs7644383	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9289640	0.83[EUR][1000 genomes]
rs9289641	0.82[JPT][hapmap]
rs963396	0.83[CHB][hapmap]
rs9848817	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9865777	0.82[JPT][hapmap]
rs9877536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877817	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs9942075	0.90[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1002446	chr3:141719169-142070290	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11706480	XRN1	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141671800-141724000	Weak transcription	Right Ventricle	heart
3	chr3:141671800-141735600	Weak transcription	Aorta	Aorta
4	chr3:141677800-141739000	Weak transcription	Left Ventricle	heart
5	chr3:141678800-141745600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:141680000-141731200	Weak transcription	Fetal Brain Female	brain
7	chr3:141680800-141723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:141682600-141723400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:141682800-141724600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:141682800-141739000	Weak transcription	Pancreas	Pancrea
11	chr3:141682800-141745800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:141682800-141746200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:141683000-141719400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:141683800-141746600	Weak transcription	Lung	lung
15	chr3:141688000-141719400	Strong transcription	Dnd41	blood
16	chr3:141688800-141720200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:141688800-141729000	Strong transcription	Fetal Thymus	thymus
18	chr3:141689400-141720000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:141691800-141722800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:141696400-141719600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:141697400-141727200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:141697600-141725800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:141698400-141721400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:141698600-141738800	Weak transcription	HSMM	muscle
25	chr3:141704200-141725400	Weak transcription	Spleen	Spleen
26	chr3:141706400-141746200	Weak transcription	Fetal Lung	lung
27	chr3:141707200-141734400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:141708400-141731200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:141708600-141728400	Weak transcription	Liver	Liver
30	chr3:141708600-141745200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:141709000-141719600	Weak transcription	Fetal Stomach	stomach
32	chr3:141709600-141721800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:141710800-141719800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:141711800-141732400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:141713000-141722400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:141713000-141724400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:141713200-141720000	Weak transcription	K562	blood
38	chr3:141713200-141722800	Weak transcription	Primary B cells from cord blood	blood
39	chr3:141713600-141721200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:141714200-141722800	Weak transcription	Adipose Nuclei	Adipose
41	chr3:141715600-141719400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:141715800-141723200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:141716000-141719600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:141716000-141720000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:141716000-141722400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:141716000-141722400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:141716000-141723000	Weak transcription	HSMMtube	muscle
48	chr3:141716000-141724600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:141716000-141732400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:141716000-141738600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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