Variant report

Variant	rs13069450
Chromosome Location	chr3:28329846-28329847
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:28282547..28284660-chr3:28329790..28333185,3	K562	blood:
2	chr3:28326784..28329887-chr3:28341556..28344967,4	K562	blood:
3	chr3:28282547..28285293-chr3:28328577..28331290,2	K562	blood:
4	chr3:28324669..28327631-chr3:28328520..28331912,3	K562	blood:

Variant related genes	Relation type
ENSG00000187118	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10510610	0.86[CEU][hapmap]
rs11129314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs11129317	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11708635	0.80[EUR][1000 genomes]
rs12106746	0.87[CEU][hapmap]
rs12106806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107183	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs12107556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374021	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12485652	0.86[CEU][hapmap]
rs12488712	0.86[CEU][hapmap]
rs12491905	0.87[CEU][hapmap]
rs12493720	0.87[CEU][hapmap]
rs12493797	0.86[CEU][hapmap]
rs12495684	0.86[CEU][hapmap]
rs13068978	0.87[CEU][hapmap]
rs13074515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs13085236	0.84[EUR][1000 genomes]
rs13085477	0.84[EUR][1000 genomes]
rs13095609	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13099977	0.94[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1599951	0.88[AMR][1000 genomes]
rs17639954	0.87[CEU][hapmap]
rs1870258	0.86[CEU][hapmap]
rs34109684	0.87[EUR][1000 genomes]
rs34335277	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34463163	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34539152	0.86[CEU][hapmap]
rs34914936	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35374336	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35504778	0.87[EUR][1000 genomes]
rs35813951	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4393865	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4552313	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4680746	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs4680912	0.92[CEU][hapmap]
rs62251110	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62251112	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6780084	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs6786752	0.86[CEU][hapmap]
rs6794980	1.00[CHB][hapmap]
rs6795634	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs6799435	0.80[CEU][hapmap]
rs6805638	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6809706	1.00[CHB][hapmap]
rs6809917	1.00[CHB][hapmap]
rs7624015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28303600-28340600	Weak transcription	NHEK	skin
2	chr3:28304200-28332400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:28306400-28332400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:28306600-28335800	Weak transcription	Hela-S3	cervix
5	chr3:28309000-28336600	Weak transcription	HUVEC	blood vessel
6	chr3:28314200-28332400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:28314400-28332400	Weak transcription	Ovary	ovary
8	chr3:28314400-28365400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:28314600-28332600	Weak transcription	Left Ventricle	heart
10	chr3:28314800-28343400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:28315000-28332400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:28315000-28333000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:28315000-28363000	Weak transcription	A549	lung
14	chr3:28315200-28332200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:28315600-28332400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:28315600-28332400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:28315600-28332400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:28315800-28332200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:28315800-28332200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:28315800-28332400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:28316000-28332000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:28316200-28333200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:28316400-28332000	Weak transcription	K562	blood
24	chr3:28317200-28332200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:28317400-28332000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr3:28317400-28332400	Weak transcription	HSMM	muscle
27	chr3:28317400-28337200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr3:28317600-28331800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:28317600-28331800	Weak transcription	GM12878-XiMat	blood
30	chr3:28317600-28332200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:28317600-28332400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:28317600-28332400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:28317600-28332400	Weak transcription	Lung	lung
34	chr3:28317600-28332400	Weak transcription	Thymus	Thymus
35	chr3:28317600-28337000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:28317600-28337000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:28317600-28337200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:28317600-28337600	Weak transcription	Fetal Intestine Large	intestine
39	chr3:28317600-28341200	Weak transcription	Fetal Thymus	thymus
40	chr3:28317600-28380000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
42	chr3:28317800-28331800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:28317800-28332400	Weak transcription	Fetal Stomach	stomach
44	chr3:28317800-28332400	Weak transcription	Right Ventricle	heart
45	chr3:28317800-28337200	Weak transcription	Fetal Intestine Small	intestine
46	chr3:28317800-28343000	Weak transcription	HepG2	liver
47	chr3:28318600-28332200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:28319600-28331800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr3:28320800-28331800	Weak transcription	Primary B cells from cord blood	blood
50	chr3:28321800-28332200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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