Variant report

Variant	rs13090606
Chromosome Location	chr3:69113153-69113154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:69109903..69113240-chr3:69128307..69131122,3	K562	blood:
2	chr3:69110772..69113240-chr3:69126872..69131199,4	K562	blood:
3	chr3:69112430..69115275-chr3:69125875..69130297,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144744	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10489	0.93[CHB][hapmap]
rs1051901	0.86[CHB][hapmap];0.81[CHD][hapmap];0.80[MKK][hapmap]
rs10865642	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11128107	0.88[CEU][hapmap];0.80[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13072064	0.81[TSI][hapmap]
rs13085120	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13099820	0.81[ASN][1000 genomes]
rs2009602	0.93[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2271118	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271120	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2271122	0.83[CEU][hapmap];0.93[CHB][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2279936	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2292199	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35718539	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3755717	0.80[EUR][1000 genomes]
rs3772979	0.93[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs3772980	0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.83[MKK][hapmap]
rs3796213	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs3821562	0.93[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3853157	0.93[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs56156415	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58950441	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6549162	0.86[EUR][1000 genomes]
rs6549163	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6549164	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6549165	0.81[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6549167	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6549169	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6549181	0.88[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6549184	0.93[CHB][hapmap]
rs6775065	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6777032	0.93[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6782474	0.86[CHB][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap]
rs6804833	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6807701	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs714300	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7426798	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7430692	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7432824	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7434153	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7611878	0.88[CEU][hapmap];0.80[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7614090	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7625579	0.93[CHB][hapmap]
rs9813514	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs9853259	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9857898	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9873272	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[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	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv520488	chr3:69104752-69114005	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv876934	chr3:69111512-69166895	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69101400-69127000	Weak transcription	Small Intestine	intestine
2	chr3:69101800-69128400	Weak transcription	Aorta	Aorta
3	chr3:69102000-69113200	Strong transcription	HSMM	muscle
4	chr3:69102000-69128200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:69102000-69128400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:69102200-69113200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:69102200-69113400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:69102200-69114000	Strong transcription	NH-A	brain
9	chr3:69102200-69127200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:69102400-69113200	Strong transcription	Placenta	Placenta
11	chr3:69102400-69116400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:69102800-69113600	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:69102800-69113800	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:69102800-69116600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:69103200-69113800	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:69103600-69116200	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:69103800-69113400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:69103800-69113800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:69104000-69113400	Strong transcription	NHDF-Ad	bronchial
20	chr3:69104000-69113600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:69104000-69113800	Strong transcription	HUVEC	blood vessel
22	chr3:69104200-69113400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:69104400-69113400	Strong transcription	Fetal Intestine Large	intestine
24	chr3:69106200-69113400	Strong transcription	Fetal Lung	lung
25	chr3:69107400-69113600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr3:69107400-69115600	Strong transcription	Liver	Liver
27	chr3:69107600-69113400	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr3:69107600-69113600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:69107800-69113600	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr3:69107800-69115000	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:69108000-69113600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:69108200-69113200	Strong transcription	GM12878-XiMat	blood
33	chr3:69108400-69128200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:69108600-69117000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:69108600-69121600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr3:69108600-69121600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr3:69108800-69113400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:69108800-69115000	Strong transcription	Primary B cells from cord blood	blood
39	chr3:69109200-69114800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr3:69109200-69118000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:69109200-69121600	Weak transcription	Fetal Brain Male	brain
42	chr3:69110200-69127000	Weak transcription	Hela-S3	cervix
43	chr3:69110400-69120000	Weak transcription	HepG2	liver
44	chr3:69110400-69122000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:69110600-69127000	Weak transcription	Brain Angular Gyrus	brain
46	chr3:69110600-69127600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:69110600-69128200	Weak transcription	Right Ventricle	heart
48	chr3:69110600-69128400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:69110600-69128400	Weak transcription	Gastric	stomach
50	chr3:69110600-69128400	Weak transcription	Psoas Muscle	Psoas

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