Variant report

Variant	rs9872199
Chromosome Location	chr3:69225875-69225876
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11128118	0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11712024	0.83[CHB][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12494541	0.80[ASN][1000 genomes]
rs12637416	0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap]
rs13059488	0.81[JPT][hapmap]
rs13059687	0.81[JPT][hapmap]
rs13082480	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28529735	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4282065	0.81[ASN][1000 genomes]
rs4450819	0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4464459	1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.82[MKK][hapmap];0.83[ASN][1000 genomes]
rs4473559	1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4493438	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4508786	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4508787	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4541413	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4624565	0.81[JPT][hapmap]
rs4855298	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855360	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56993809	0.91[AMR][1000 genomes]
rs57343254	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57396300	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61312273	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6763046	0.83[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6765197	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6804718	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72930216	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930219	0.88[AMR][1000 genomes]
rs7609655	0.81[ASN][1000 genomes]
rs9310138	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9310139	0.81[ASN][1000 genomes]
rs9310140	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9831516	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9833167	0.80[JPT][hapmap]
rs9836305	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9838728	0.81[JPT][hapmap]
rs9847983	0.81[JPT][hapmap]
rs9853318	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9853587	0.85[CHB][hapmap];0.90[CHD][hapmap];0.89[MEX][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9853744	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9872489	0.83[ASN][1000 genomes]
rs9875511	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69209600-69228000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:69211200-69226600	Weak transcription	Fetal Kidney	kidney
3	chr3:69211200-69229400	Weak transcription	Fetal Brain Male	brain
4	chr3:69211600-69230200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:69211600-69231000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:69214200-69226600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:69214800-69230400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:69216000-69227200	Weak transcription	Pancreas	Pancrea
9	chr3:69216200-69229800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:69217200-69230200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:69217400-69229800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:69217600-69227400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:69217600-69230600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:69218400-69230000	Weak transcription	Hela-S3	cervix
15	chr3:69218400-69247400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:69218400-69247800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:69218600-69228000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:69218600-69228200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:69218600-69228400	Weak transcription	Adipose Nuclei	Adipose
20	chr3:69218800-69227600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:69218800-69228400	Weak transcription	Colonic Mucosa	Colon
22	chr3:69219000-69227200	Weak transcription	Small Intestine	intestine
23	chr3:69219200-69230000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:69219400-69226000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr3:69219400-69227000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:69219600-69227000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:69219800-69230800	Strong transcription	Placenta	Placenta
28	chr3:69220600-69229600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:69220800-69229800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:69220800-69231600	Weak transcription	Psoas Muscle	Psoas
31	chr3:69221000-69227000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:69221000-69227000	Weak transcription	Gastric	stomach
33	chr3:69221000-69227000	Weak transcription	Thymus	Thymus
34	chr3:69221000-69227400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:69221000-69227400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:69221000-69228200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:69221000-69229400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:69221000-69230000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:69221200-69226600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:69221200-69227200	Weak transcription	Right Ventricle	heart
41	chr3:69221200-69227400	Weak transcription	Fetal Heart	heart
42	chr3:69221200-69229400	Weak transcription	Left Ventricle	heart
43	chr3:69221200-69229800	Weak transcription	Aorta	Aorta
44	chr3:69221400-69227200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:69221400-69229000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:69222000-69229400	Weak transcription	HSMM	muscle
47	chr3:69222200-69227000	Weak transcription	HMEC	breast
48	chr3:69222400-69227000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:69222800-69237400	Strong transcription	Dnd41	blood
50	chr3:69222800-69245400	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links