Variant report

Variant	rs3088062
Chromosome Location	chr1:47844017-47844018
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	chr1:47834279..47838384-chr1:47842508..47846874,4	K562	blood:

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10157883	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10399673	0.81[JPT][hapmap]
rs10789507	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10890475	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10890476	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10890477	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10890478	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211504	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11211508	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11211513	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.88[ASN][1000 genomes]
rs11211517	0.95[JPT][hapmap]
rs11211520	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211521	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11211522	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211523	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211524	0.95[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11578038	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11582877	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12024163	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12039726	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12040451	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12042624	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12047319	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12048407	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12409549	0.87[ASN][1000 genomes]
rs12566521	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2246707	0.82[ASN][1000 genomes]
rs2249665	0.90[MEX][hapmap]
rs2306470	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406102	0.80[EUR][1000 genomes]
rs2406105	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2472725	0.95[JPT][hapmap]
rs2472730	0.81[ASN][1000 genomes]
rs2494246	0.92[ASN][1000 genomes]
rs2622901	0.81[ASN][1000 genomes]
rs2622905	0.82[ASN][1000 genomes]
rs2622908	0.82[ASN][1000 genomes]
rs2622925	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2742099	0.81[ASN][1000 genomes]
rs2742103	0.84[ASN][1000 genomes]
rs2742104	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2758735	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2758744	0.84[ASN][1000 genomes]
rs2798349	0.95[MEX][hapmap]
rs2820983	0.80[EUR][1000 genomes]
rs2820987	0.82[ASN][1000 genomes]
rs2820988	0.82[ASN][1000 genomes]
rs2820989	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2821088	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2821089	0.82[ASN][1000 genomes]
rs2821093	0.95[JPT][hapmap]
rs2897237	0.81[ASN][1000 genomes]
rs3122607	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3122610	0.82[ASN][1000 genomes]
rs3122611	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3122615	0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs3122616	0.85[ASN][1000 genomes]
rs3122619	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3122623	0.83[ASN][1000 genomes]
rs3125624	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs3125628	0.90[JPT][hapmap]
rs3125630	0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs3125631	0.85[ASN][1000 genomes]
rs3125632	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3125633	0.95[JPT][hapmap]
rs3125635	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.87[ASN][1000 genomes]
rs3125636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3125644	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.84[ASN][1000 genomes]
rs3814003	0.83[CEU][hapmap];0.91[EUR][1000 genomes]
rs3925058	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs4492666	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4600090	1.00[MEX][hapmap];1.00[YRI][hapmap]
rs4603175	0.81[JPT][hapmap]
rs4926836	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4926839	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56987466	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58688029	0.84[ASN][1000 genomes]
rs59492977	0.84[ASN][1000 genomes]
rs61284456	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61782712	0.84[ASN][1000 genomes]
rs61782733	0.86[ASN][1000 genomes]
rs61784774	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6588348	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs6588365	0.81[ASN][1000 genomes]
rs6660321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6662189	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6662814	0.81[ASN][1000 genomes]
rs6671254	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs6673882	0.81[JPT][hapmap]
rs6690084	1.00[MEX][hapmap];1.00[YRI][hapmap]
rs6697248	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.85[ASN][1000 genomes]
rs7511699	0.85[ASN][1000 genomes]
rs7525650	0.95[JPT][hapmap]
rs7532148	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs7534571	1.00[YRI][hapmap]
rs7541522	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7545281	0.87[ASN][1000 genomes]
rs9436394	0.85[ASN][1000 genomes]
rs9436429	0.85[ASN][1000 genomes]
rs9436430	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs9436882	0.90[CHB][hapmap];1.00[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	nsv947182	chr1:47841662-47845531	Strong transcription Genic enhancers Weak transcription Active TSS Enhancers	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3088062	CMPK1	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47800600-47854600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:47801000-47850800	Weak transcription	NHEK	skin
3	chr1:47814800-47850600	Weak transcription	Aorta	Aorta
4	chr1:47823000-47846400	Weak transcription	Colonic Mucosa	Colon
5	chr1:47824000-47851000	Weak transcription	Stomach Mucosa	stomach
6	chr1:47824000-47853800	Weak transcription	Psoas Muscle	Psoas
7	chr1:47827800-47854800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:47832200-47854200	Weak transcription	Esophagus	oesophagus
9	chr1:47833200-47852000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:47833400-47844600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:47833600-47854200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:47833600-47854200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:47834000-47847400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:47834000-47847600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:47834000-47847600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:47834000-47849200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:47834000-47849200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:47834000-47849200	Strong transcription	Dnd41	blood
19	chr1:47834000-47849400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:47834200-47847000	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr1:47834200-47847600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr1:47834200-47847600	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:47834200-47848000	Strong transcription	HSMM	muscle
24	chr1:47834200-47849200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:47834200-47849400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:47834200-47849400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr1:47834200-47849400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:47834200-47850200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:47835000-47844600	Weak transcription	Lung	lung
30	chr1:47835000-47846600	Weak transcription	Gastric	stomach
31	chr1:47835200-47844600	Weak transcription	Spleen	Spleen
32	chr1:47835200-47844800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:47835200-47853400	Weak transcription	NHLF	lung
34	chr1:47835200-47853600	Weak transcription	Fetal Brain Male	brain
35	chr1:47835400-47849800	Weak transcription	Fetal Heart	heart
36	chr1:47835400-47853200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:47836000-47846600	Weak transcription	Brain Anterior Caudate	brain
38	chr1:47836000-47850200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:47836400-47846400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:47836400-47854400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:47836600-47852800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:47836600-47854800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:47837000-47845000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:47837000-47845200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:47837000-47846400	Weak transcription	Small Intestine	intestine
46	chr1:47837200-47846400	Weak transcription	Fetal Kidney	kidney
47	chr1:47837200-47847600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:47837200-47853200	Weak transcription	A549	lung
49	chr1:47837600-47844600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:47839000-47844600	Weak transcription	Thymus	Thymus

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