Variant report

Variant	rs1492489
Chromosome Location	chr3:111841303-111841304
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	chr3:111833855..111836501-chr3:111839924..111841508,2	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10511304	1.00[CHB][hapmap]
rs10511310	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs10934163	1.00[CHB][hapmap]
rs10934164	1.00[CHB][hapmap]
rs11926389	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12489470	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs12489616	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12497979	1.00[CHB][hapmap]
rs12636943	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13063452	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs13064242	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs13084103	1.00[CHB][hapmap]
rs1388858	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1388859	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17444215	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17446282	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs17505536	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs1873712	1.00[ASN][1000 genomes]
rs4234409	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs4234410	1.00[ASN][1000 genomes]
rs4234411	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs4280608	1.00[ASN][1000 genomes]
rs4321508	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4347976	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs4422273	1.00[ASN][1000 genomes]
rs4434123	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs4498008	1.00[ASN][1000 genomes]
rs4507228	1.00[ASN][1000 genomes]
rs4538347	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4564946	1.00[ASN][1000 genomes]
rs4622877	0.82[CEU][hapmap]
rs4638935	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4682087	1.00[ASN][1000 genomes]
rs4682092	1.00[ASN][1000 genomes]
rs4682367	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs4682373	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs55714509	1.00[ASN][1000 genomes]
rs55869871	1.00[ASN][1000 genomes]
rs55899888	1.00[ASN][1000 genomes]
rs56042414	1.00[ASN][1000 genomes]
rs56062310	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56109455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56129827	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56353930	1.00[ASN][1000 genomes]
rs62276971	1.00[ASN][1000 genomes]
rs62276973	1.00[ASN][1000 genomes]
rs62276974	1.00[ASN][1000 genomes]
rs62277010	1.00[ASN][1000 genomes]
rs62277011	1.00[ASN][1000 genomes]
rs62277480	1.00[ASN][1000 genomes]
rs62280198	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62280199	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62280204	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62280205	1.00[ASN][1000 genomes]
rs6438037	1.00[ASN][1000 genomes]
rs6438038	1.00[ASN][1000 genomes]
rs6770357	1.00[ASN][1000 genomes]
rs6772480	1.00[ASN][1000 genomes]
rs6781207	1.00[ASN][1000 genomes]
rs6781215	1.00[ASN][1000 genomes]
rs6781683	1.00[ASN][1000 genomes]
rs6781844	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs6787323	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6789875	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6795820	1.00[CHB][hapmap]
rs6797177	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs6801795	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6804836	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs6805112	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6805397	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6805505	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs6805887	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs73218074	1.00[ASN][1000 genomes]
rs73218079	1.00[ASN][1000 genomes]
rs73223686	1.00[ASN][1000 genomes]
rs732686	1.00[CHB][hapmap]
rs7431999	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs7432037	1.00[ASN][1000 genomes]
rs744661	0.81[LWK][hapmap]
rs7615460	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7621219	1.00[ASN][1000 genomes]
rs7621431	1.00[CHB][hapmap]
rs7625249	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7631223	1.00[ASN][1000 genomes]
rs7636107	1.00[CHB][hapmap]
rs7637676	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs7637682	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs9288939	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs9288942	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs9810170	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9810421	1.00[CHB][hapmap]
rs9811691	1.00[CHB][hapmap]
rs9813882	1.00[ASN][1000 genomes]
rs9819540	1.00[ASN][1000 genomes]
rs9838986	1.00[ASN][1000 genomes]
rs9855755	1.00[CHB][hapmap]
rs9871492	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9871532	1.00[ASN][1000 genomes]
rs9877734	1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1492489	CD200	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111810400-111852000	Weak transcription	Esophagus	oesophagus
2	chr3:111812000-111844000	Weak transcription	Colonic Mucosa	Colon
3	chr3:111812000-111845600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:111812200-111853000	Weak transcription	Right Ventricle	heart
5	chr3:111819600-111847800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:111821200-111843600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:111821400-111843600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:111822000-111844600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:111825800-111844400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:111830600-111853200	Weak transcription	Lung	lung
11	chr3:111830800-111845400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:111831400-111843000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:111832000-111844600	Weak transcription	Hela-S3	cervix
14	chr3:111832600-111841600	Enhancers	Primary B cells from peripheral blood	blood
15	chr3:111833200-111844000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:111834200-111853800	Weak transcription	Fetal Intestine Small	intestine
17	chr3:111834400-111848000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:111834600-111841600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:111835800-111844400	Weak transcription	Fetal Heart	heart
20	chr3:111835800-111849600	Weak transcription	Small Intestine	intestine
21	chr3:111836200-111843600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:111836200-111844200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:111836200-111845000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:111836200-111849200	Weak transcription	Aorta	Aorta
25	chr3:111836600-111846400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:111837800-111842200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:111838400-111845400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:111838600-111842000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:111838800-111843800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:111838800-111844400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr3:111838800-111845400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:111839000-111843600	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:111839000-111843800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:111839000-111843800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:111839000-111844200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:111839000-111845200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:111839000-111845200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:111839000-111845600	Weak transcription	Adipose Nuclei	Adipose
39	chr3:111839000-111853000	Weak transcription	Left Ventricle	heart
40	chr3:111839200-111842000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:111839200-111842400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:111839200-111843600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:111839200-111843800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:111839400-111844000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:111839600-111841800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:111839600-111842000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:111839600-111843600	Weak transcription	HSMMtube	muscle
48	chr3:111839600-111845400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:111839600-111847400	Weak transcription	HMEC	breast
50	chr3:111839800-111841400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links