Variant report

Variant	rs4894948
Chromosome Location	chr3:105477692-105477693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1020327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1025885	1.00[AMR][1000 genomes]
rs1025886	1.00[AMR][1000 genomes]
rs1036877	1.00[AMR][1000 genomes]
rs1039545	1.00[AMR][1000 genomes]
rs10933832	1.00[AMR][1000 genomes]
rs1348348	1.00[AMR][1000 genomes]
rs1443099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1443107	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1503922	1.00[AMR][1000 genomes]
rs1548056	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1561920	1.00[AMR][1000 genomes]
rs1822348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1838045	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1867428	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1867429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1963622	1.00[AMR][1000 genomes]
rs1992520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2197351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2221379	1.00[AMR][1000 genomes]
rs3862049	1.00[AMR][1000 genomes]
rs4243428	1.00[AMR][1000 genomes]
rs4282093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4613490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4894945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4894947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4894959	1.00[AMR][1000 genomes]
rs4894961	1.00[AMR][1000 genomes]
rs6437615	1.00[AMR][1000 genomes]
rs6437617	1.00[AMR][1000 genomes]
rs6437625	1.00[AMR][1000 genomes]
rs6765716	1.00[AMR][1000 genomes]
rs6768096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6804286	1.00[AMR][1000 genomes]
rs6805675	1.00[AMR][1000 genomes]
rs7622735	1.00[AMR][1000 genomes]
rs7643647	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7649437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9288816	1.00[AMR][1000 genomes]
rs9288819	1.00[AMR][1000 genomes]
rs9288820	1.00[AMR][1000 genomes]
rs976961	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs976962	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9809911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9811870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs981479	1.00[AMR][1000 genomes]
rs9830539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9831221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9833645	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9838768	1.00[AMR][1000 genomes]
rs9859644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9872290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877306	chr3:105372196-105495841	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv877308	chr3:105373836-105495841	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv877310	chr3:105409321-105495841	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv591244	chr3:105438320-105495841	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv591246	chr3:105439522-105504129	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv877311	chr3:105449986-105493286	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105464200-105478200	Weak transcription	Right Atrium	heart
2	chr3:105464800-105482600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:105465600-105478200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:105465800-105483400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:105466000-105481200	Weak transcription	Fetal Kidney	kidney
6	chr3:105466600-105481400	Weak transcription	HepG2	liver
7	chr3:105467600-105478000	Weak transcription	Colonic Mucosa	Colon
8	chr3:105467600-105480800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:105467600-105509400	Weak transcription	Stomach Mucosa	stomach
10	chr3:105472000-105477800	Weak transcription	Thymus	Thymus
11	chr3:105472200-105477800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:105472200-105499000	Weak transcription	NHDF-Ad	bronchial
13	chr3:105472400-105504400	Weak transcription	HUVEC	blood vessel
14	chr3:105472600-105478600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr3:105472800-105480200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:105473000-105477800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr3:105473000-105481400	Weak transcription	NH-A	brain
18	chr3:105473400-105477800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:105473800-105478800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:105474600-105483200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:105474800-105478400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:105475200-105483000	Strong transcription	Osteobl	bone
23	chr3:105475200-105485600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:105475400-105478400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:105475600-105478800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:105475800-105483000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:105476000-105486600	Weak transcription	Psoas Muscle	Psoas
28	chr3:105476200-105480400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:105476400-105480400	Weak transcription	Small Intestine	intestine
30	chr3:105476400-105480600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:105476600-105478800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:105477000-105477800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:105477000-105478600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr3:105477000-105478800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:105477000-105478800	Genic enhancers	Primary T cells from cord blood	blood
36	chr3:105477000-105481200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:105477200-105478800	ZNF genes & repeats	Primary B cells from cord blood	blood
38	chr3:105477200-105478800	Genic enhancers	Primary T cells fromperipheralblood	blood
39	chr3:105477200-105478800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
40	chr3:105477200-105478800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:105477200-105478800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
42	chr3:105477200-105478800	ZNF genes & repeats	Esophagus	oesophagus
43	chr3:105477200-105478800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
44	chr3:105477200-105478800	ZNF genes & repeats	Fetal Thymus	thymus
45	chr3:105477200-105478800	Genic enhancers	Left Ventricle	heart
46	chr3:105477200-105478800	ZNF genes & repeats	Spleen	Spleen
47	chr3:105477200-105478800	ZNF genes & repeats	GM12878-XiMat	blood
48	chr3:105477200-105479000	ZNF genes & repeats	Fetal Intestine Small	intestine
49	chr3:105477400-105477800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:105477400-105477800	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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