Variant report

Variant	rs11569216
Chromosome Location	chr3:141701527-141701528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141085243..141087271-chr3:141699890..141701826,2	K562	blood:

Variant related genes	Relation type
ENSG00000177311	Chromatin interaction
ENSG00000249417	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11569198	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11569256	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12495978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13069749	0.95[ASN][1000 genomes]
rs1543064	0.94[CHB][hapmap];0.80[CHD][hapmap];0.93[JPT][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs1705612	0.87[JPT][hapmap]
rs1705613	0.87[JPT][hapmap]
rs1820941	0.90[ASN][1000 genomes]
rs2063453	0.86[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2063454	0.86[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271386	0.86[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2861421	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2862122	0.91[ASN][1000 genomes]
rs34092379	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34464850	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34486172	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34514405	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34579489	0.93[ASN][1000 genomes]
rs34773643	0.87[EUR][1000 genomes]
rs35486283	0.93[ASN][1000 genomes]
rs35787200	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3811708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3817176	0.86[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4315664	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4315665	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683417	0.91[ASN][1000 genomes]
rs56129773	0.93[ASN][1000 genomes]
rs62283132	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440054	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6764833	0.88[ASN][1000 genomes]
rs6778085	0.94[CHB][hapmap];0.80[CHD][hapmap];0.93[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs6795301	0.94[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs6795500	0.88[ASN][1000 genomes]
rs6803884	0.91[ASN][1000 genomes]
rs6806443	0.91[ASN][1000 genomes]
rs7426584	0.87[JPT][hapmap]
rs7611705	0.87[JPT][hapmap]
rs7619506	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7630837	0.82[ASN][1000 genomes]
rs7633321	0.85[ASN][1000 genomes]
rs7644383	0.82[CHB][hapmap]
rs907293	0.91[ASN][1000 genomes]
rs9289641	0.88[CHB][hapmap];0.93[JPT][hapmap];0.83[TSI][hapmap]
rs963396	0.94[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs9815587	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9863685	0.88[ASN][1000 genomes]
rs9865777	0.87[CHB][hapmap];0.93[JPT][hapmap];0.83[TSI][hapmap]
rs9880805	0.88[ASN][1000 genomes]
rs9942	0.85[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11569216	XRN1	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141671800-141719000	Weak transcription	Placenta	Placenta
3	chr3:141671800-141724000	Weak transcription	Right Ventricle	heart
4	chr3:141671800-141735600	Weak transcription	Aorta	Aorta
5	chr3:141674400-141708000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:141674600-141712600	Weak transcription	Fetal Brain Male	brain
7	chr3:141676200-141703800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:141677800-141739000	Weak transcription	Left Ventricle	heart
9	chr3:141678800-141745600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:141680000-141711200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:141680000-141731200	Weak transcription	Fetal Brain Female	brain
12	chr3:141680800-141723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:141682000-141711200	Weak transcription	GM12878-XiMat	blood
14	chr3:141682600-141723400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:141682800-141712200	Weak transcription	Ovary	ovary
16	chr3:141682800-141724600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:141682800-141739000	Weak transcription	Pancreas	Pancrea
18	chr3:141682800-141745800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:141682800-141746200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr3:141683000-141719400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:141683200-141709800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:141683600-141716200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:141683800-141704600	Weak transcription	Brain Germinal Matrix	brain
24	chr3:141683800-141746600	Weak transcription	Lung	lung
25	chr3:141688000-141702000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:141688000-141704800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:141688000-141719400	Strong transcription	Dnd41	blood
28	chr3:141688400-141714600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:141688800-141706200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:141688800-141711200	Weak transcription	Fetal Kidney	kidney
31	chr3:141688800-141720200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:141688800-141729000	Strong transcription	Fetal Thymus	thymus
33	chr3:141689400-141706800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:141689400-141720000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:141691400-141712200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:141691600-141706000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:141691600-141708000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:141691800-141703400	Weak transcription	Primary T cells from cord blood	blood
39	chr3:141691800-141711200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:141691800-141711400	Weak transcription	Primary B cells from cord blood	blood
41	chr3:141691800-141722800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:141692600-141712800	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:141693200-141712600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:141694000-141704200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:141695600-141706400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:141695600-141712600	Weak transcription	Adipose Nuclei	Adipose
47	chr3:141695800-141705400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:141696400-141707600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:141696400-141719600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:141697200-141706400	Weak transcription	Fetal Stomach	stomach

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