Variant report

Variant	rs9864729
Chromosome Location	chr3:48579736-48579737
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	chr3:48579149..48580932-chr3:48582283..48584303,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10049154	0.82[ASN][1000 genomes]
rs10470687	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13060933	0.94[ASN][1000 genomes]
rs13062576	0.84[ASN][1000 genomes]
rs13064619	0.82[ASN][1000 genomes]
rs13091944	0.98[ASN][1000 genomes]
rs13094578	0.86[ASN][1000 genomes]
rs13100178	0.86[ASN][1000 genomes]
rs13319635	0.94[ASN][1000 genomes]
rs13319651	0.94[ASN][1000 genomes]
rs2006871	0.98[ASN][1000 genomes]
rs2854394	0.88[ASN][1000 genomes]
rs2854395	0.88[ASN][1000 genomes]
rs28563843	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581474	0.86[ASN][1000 genomes]
rs28881595	0.81[ASN][1000 genomes]
rs35343040	0.80[ASN][1000 genomes]
rs35562294	0.92[ASN][1000 genomes]
rs3755819	0.95[ASN][1000 genomes]
rs3969942	0.86[ASN][1000 genomes]
rs4075082	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442127	0.85[ASN][1000 genomes]
rs6765317	0.80[ASN][1000 genomes]
rs6781283	0.94[ASN][1000 genomes]
rs6785845	0.82[ASN][1000 genomes]
rs6792156	0.82[ASN][1000 genomes]
rs6792525	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6806059	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6809981	0.82[ASN][1000 genomes]
rs7428949	0.86[ASN][1000 genomes]
rs7434077	0.86[ASN][1000 genomes]
rs7434107	0.86[ASN][1000 genomes]
rs7623614	0.86[ASN][1000 genomes]
rs7640031	0.86[ASN][1000 genomes]
rs7644771	0.86[ASN][1000 genomes]
rs9810549	1.00[ASN][1000 genomes]
rs9810991	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816942	0.86[ASN][1000 genomes]
rs9822677	0.82[ASN][1000 genomes]
rs9830581	0.80[ASN][1000 genomes]
rs9835827	0.82[ASN][1000 genomes]
rs9835902	0.85[ASN][1000 genomes]
rs9837687	1.00[ASN][1000 genomes]
rs9843316	0.80[ASN][1000 genomes]
rs9848824	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849280	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850102	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9851743	0.86[ASN][1000 genomes]
rs9851771	0.86[ASN][1000 genomes]
rs9869698	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871180	0.91[ASN][1000 genomes]
rs9871608	0.86[ASN][1000 genomes]
rs9878950	0.94[ASN][1000 genomes]
rs9881877	0.92[ASN][1000 genomes]
rs9882962	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48547600-48591600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:48555200-48582200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:48556200-48580400	Weak transcription	HSMMtube	muscle
4	chr3:48556200-48586800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:48556400-48586400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:48559600-48586400	Weak transcription	Primary B cells from cord blood	blood
7	chr3:48562600-48592000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:48565800-48583600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:48568800-48586000	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:48570400-48580600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:48570600-48591600	Weak transcription	Fetal Brain Male	brain
12	chr3:48571000-48581800	Strong transcription	Fetal Intestine Small	intestine
13	chr3:48571400-48580600	Weak transcription	Left Ventricle	heart
14	chr3:48572200-48583800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr3:48572600-48579800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:48572600-48581800	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr3:48572800-48580400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:48573400-48580600	Weak transcription	Adipose Nuclei	Adipose
19	chr3:48573400-48584400	Weak transcription	Fetal Kidney	kidney
20	chr3:48573600-48580600	Weak transcription	HSMM	muscle
21	chr3:48573600-48583600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:48573600-48589600	Weak transcription	Fetal Lung	lung
23	chr3:48573600-48592600	Weak transcription	NHDF-Ad	bronchial
24	chr3:48573600-48593400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:48573800-48580200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:48574000-48580400	Weak transcription	Right Ventricle	heart
27	chr3:48574000-48583400	Weak transcription	Aorta	Aorta
28	chr3:48574000-48583400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:48574200-48586000	Weak transcription	Primary T cells from cord blood	blood
30	chr3:48574400-48580400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:48574400-48583400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:48574400-48583400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:48574400-48591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:48574800-48580400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:48574800-48580600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:48574800-48583600	Weak transcription	NH-A	brain
37	chr3:48574800-48591200	Weak transcription	Dnd41	blood
38	chr3:48575000-48580400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:48576000-48580200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:48576000-48594000	Weak transcription	Small Intestine	intestine
41	chr3:48576200-48580000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr3:48576200-48583600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:48576400-48583400	Weak transcription	Brain Angular Gyrus	brain
44	chr3:48576400-48583400	Weak transcription	A549	lung
45	chr3:48576400-48590200	Weak transcription	Colonic Mucosa	Colon
46	chr3:48576400-48591800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:48576600-48583200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:48576600-48583600	Weak transcription	Osteobl	bone
49	chr3:48576800-48580400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:48576800-48583600	Weak transcription	Primary hematopoietic stem cells	blood

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