Variant report

Variant	rs10512909
Chromosome Location	chr3:133368199-133368200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10512903	1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512904	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512907	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512908	0.95[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706413	0.95[CEU][hapmap];1.00[GIH][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706586	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706809	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707750	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708197	0.95[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708532	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708565	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709132	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709349	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709404	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709461	0.84[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709940	0.94[CEU][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710111	0.89[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710717	1.00[ASN][1000 genomes]
rs11711706	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712186	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11712672	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713205	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713248	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714392	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714422	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715407	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715435	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715615	0.95[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716197	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716388	0.95[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716415	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717424	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717902	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718050	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718234	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718255	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719366	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719585	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720825	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17301253	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17301521	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17301766	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17301889	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17373504	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17373726	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2718801	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28846461	0.80[AMR][1000 genomes]
rs55729127	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55741097	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56040719	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56292037	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56323915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282385	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62282388	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282389	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282390	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282392	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282415	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282417	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282418	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282419	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282420	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282421	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282427	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282428	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282429	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282456	0.82[EUR][1000 genomes]
rs7349558	0.87[EUR][1000 genomes]
rs7630957	0.80[EUR][1000 genomes]
rs7650725	0.82[EUR][1000 genomes]
rs7653808	0.82[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10512909	TOPBP1	cis	cerebellum	SCAN
rs10512909	TOPBP1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133316600-133377600	Strong transcription	Dnd41	blood
2	chr3:133316600-133378000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:133317000-133378200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr3:133317200-133378800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:133318400-133378600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:133322200-133378200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:133322600-133378800	Weak transcription	Stomach Mucosa	stomach
8	chr3:133323200-133378200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:133323200-133378400	Strong transcription	Fetal Thymus	thymus
10	chr3:133323200-133378800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:133323400-133378200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:133323600-133377800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr3:133323800-133378800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:133324200-133378200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:133332200-133378600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:133333400-133378000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:133334200-133378400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:133334400-133368800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr3:133337400-133380000	Weak transcription	Pancreas	Pancrea
20	chr3:133338600-133368600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:133339800-133378000	Strong transcription	Primary B cells from cord blood	blood
22	chr3:133340200-133380000	Weak transcription	Right Ventricle	heart
23	chr3:133341200-133378800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr3:133345600-133380000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:133345600-133380000	Weak transcription	Psoas Muscle	Psoas
26	chr3:133346600-133368800	Strong transcription	GM12878-XiMat	blood
27	chr3:133349400-133369000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:133349600-133378200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:133351400-133368800	Strong transcription	Primary hematopoietic stem cells	blood
30	chr3:133352400-133378200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:133352600-133370800	Weak transcription	Lung	lung
32	chr3:133352600-133380000	Weak transcription	Esophagus	oesophagus
33	chr3:133352600-133380000	Weak transcription	Gastric	stomach
34	chr3:133352600-133380000	Weak transcription	Spleen	Spleen
35	chr3:133353000-133379800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:133353800-133378200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:133359000-133368800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:133359000-133374800	Weak transcription	Fetal Heart	heart
39	chr3:133359600-133377800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:133359600-133380000	Weak transcription	Aorta	Aorta
41	chr3:133360200-133368800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr3:133360400-133369200	Strong transcription	Fetal Intestine Large	intestine
43	chr3:133360800-133377200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:133361000-133373800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:133361200-133368200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:133361200-133368800	Strong transcription	Adipose Nuclei	Adipose
47	chr3:133361600-133368800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:133361800-133374200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:133362000-133374600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:133362200-133370400	Weak transcription	Brain Anterior Caudate	brain

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