Variant report

Variant	rs1871847
Chromosome Location	chr3:99540510-99540511
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1038295	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10804762	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485299	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12486901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491153	1.00[CEU][hapmap];0.96[GIH][hapmap];0.93[EUR][1000 genomes]
rs12493124	1.00[CEU][hapmap];0.96[GIH][hapmap];0.84[EUR][1000 genomes]
rs1492343	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1610263	0.80[CEU][hapmap]
rs1610265	0.89[CEU][hapmap];0.82[CHB][hapmap]
rs1971381	0.88[JPT][hapmap]
rs2036984	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs35590972	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732444	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3921767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4408901	0.84[JPT][hapmap]
rs4536867	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs4928143	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4928144	0.88[JPT][hapmap]
rs4928219	1.00[JPT][hapmap]
rs4928220	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[YRI][hapmap]
rs4928222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4928233	0.84[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap]
rs4928236	0.84[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap]
rs55874130	0.84[EUR][1000 genomes]
rs55964918	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56140081	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56223679	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56260910	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56335268	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60119031	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61010376	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778589	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs6792339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800456	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73858966	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73859911	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73860464	0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73860470	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7610759	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs7614366	0.80[CHD][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap]
rs7632327	0.88[JPT][hapmap]
rs7632345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634628	0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7635633	1.00[CEU][hapmap]
rs7635871	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821563	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs9827744	0.84[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap]
rs9858145	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs9872339	0.84[CHB][hapmap];0.88[JPT][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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99542400	Weak transcription	Small Intestine	intestine
2	chr3:99537200-99562600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
4	chr3:99537400-99544200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:99537400-99551000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:99537400-99552400	Weak transcription	Ovary	ovary
7	chr3:99537800-99541000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:99537800-99541000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:99537800-99542200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:99537800-99542200	Weak transcription	Stomach Mucosa	stomach
11	chr3:99537800-99542400	Weak transcription	Placenta	Placenta
12	chr3:99537800-99542600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:99537800-99543400	Weak transcription	Fetal Kidney	kidney
14	chr3:99537800-99543600	Weak transcription	HSMMtube	muscle
15	chr3:99537800-99544400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:99537800-99547600	Weak transcription	Aorta	Aorta
17	chr3:99537800-99548200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:99537800-99552400	Weak transcription	Pancreas	Pancrea
19	chr3:99537800-99561800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:99537800-99562400	Weak transcription	Left Ventricle	heart
21	chr3:99538000-99541600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:99538000-99542600	Weak transcription	Psoas Muscle	Psoas
23	chr3:99538000-99543200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:99538000-99543200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:99538000-99543200	Weak transcription	Liver	Liver
26	chr3:99538000-99543600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:99538000-99543600	Weak transcription	NHLF	lung
28	chr3:99538000-99543800	Weak transcription	A549	lung
29	chr3:99538000-99543800	Weak transcription	HSMM	muscle
30	chr3:99538000-99543800	Weak transcription	NH-A	brain
31	chr3:99538000-99544000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:99538000-99544000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:99538000-99544000	Weak transcription	NHDF-Ad	bronchial
34	chr3:99538000-99544000	Weak transcription	Osteobl	bone
35	chr3:99538000-99550400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:99538000-99550800	Weak transcription	Brain Anterior Caudate	brain
37	chr3:99538000-99552000	Weak transcription	Fetal Intestine Small	intestine
38	chr3:99538000-99552400	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:99538000-99556000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:99538000-99556800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:99538000-99563600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:99538200-99541600	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:99538200-99542200	Weak transcription	HepG2	liver
44	chr3:99538200-99542600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:99538200-99543800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:99538200-99544000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:99538200-99544000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:99538200-99544000	Weak transcription	HMEC	breast
49	chr3:99538200-99544400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:99538200-99547200	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links