Variant report

Variant	rs11211517
Chromosome Location	chr1:47798131-47798132
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:47797779-47800924	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:47652463..47655353-chr1:47795985..47798380,2	MCF-7	breast:
2	chr1:47642908..47645406-chr1:47797799..47799356,2	MCF-7	breast:
3	chr1:47772551..47781833-chr1:47797933..47806586,42	K562	blood:
4	chr1:47132421..47133961-chr1:47797739..47800236,2	K562	blood:

Variant related genes	Relation type
CMPK1	TF binding region
ENSG00000224805	Chromatin interaction
ENSG00000123473	Chromatin interaction
ENSG00000225506	Chromatin interaction
ENSG00000123472	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10157883	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1028646	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1028647	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10399673	0.85[JPT][hapmap]
rs1044457	0.82[CEU][hapmap];0.93[TSI][hapmap]
rs10789507	0.95[JPT][hapmap]
rs10890475	0.95[JPT][hapmap]
rs10890478	0.95[JPT][hapmap]
rs11211504	0.95[JPT][hapmap]
rs11211508	0.95[JPT][hapmap]
rs11211510	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211511	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211513	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11211520	0.95[JPT][hapmap]
rs11578038	0.82[ASN][1000 genomes]
rs11582877	0.95[JPT][hapmap]
rs12024163	0.81[ASN][1000 genomes]
rs12039726	0.95[JPT][hapmap]
rs12040451	0.81[ASN][1000 genomes]
rs12118514	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12121831	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12125261	1.00[CEU][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12126139	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12127982	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12132928	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12138072	0.91[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12141060	1.00[CEU][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12409549	0.80[ASN][1000 genomes]
rs12562561	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12730819	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12732050	0.91[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12732410	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12743877	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17452995	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2246707	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2405922	0.81[JPT][hapmap]
rs2472725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2494247	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2622901	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2622905	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2622907	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2622908	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2622925	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2742081	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2742104	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2758735	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2758736	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2758737	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2820971	0.81[JPT][hapmap]
rs2820987	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2820988	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2820989	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2821087	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2821088	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2821090	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2821093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2821094	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2821096	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3088062	0.95[JPT][hapmap]
rs3122607	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3122610	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3122611	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3122615	0.96[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3122619	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3122620	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3122623	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3125624	0.96[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3125625	0.82[EUR][1000 genomes]
rs3125628	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3125630	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3125632	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3125633	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3125635	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3125636	0.95[JPT][hapmap]
rs3125638	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3125639	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3125640	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3125641	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3125644	0.95[JPT][hapmap]
rs3125647	0.81[ASN][1000 genomes]
rs34400183	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34952704	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35711761	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35774681	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35880845	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3925058	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4147192	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4492666	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4603175	0.86[JPT][hapmap]
rs4926824	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4926836	0.95[JPT][hapmap]
rs55737131	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61782706	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6588348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6588365	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6659946	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6660321	0.95[JPT][hapmap]
rs6671254	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6673882	0.86[JPT][hapmap]
rs6681868	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6689687	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6692691	0.86[GIH][hapmap]
rs6692734	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6697248	0.95[JPT][hapmap]
rs6703956	1.00[CEU][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6795	0.89[CEU][hapmap]
rs71645861	0.86[EUR][1000 genomes]
rs7525650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7532148	0.95[JPT][hapmap]
rs7541748	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7543016	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7545281	0.80[ASN][1000 genomes]
rs9436430	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9436749	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9436838	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9436882	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	esv3390574	chr1:47778981-47803091	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11211517	MKNK1	cis	cerebellum	SCAN
rs11211517	CMPK1	cis	lymphoblastoid	seeQTL
rs11211517	CMPK	Cis_1M	lymphoblastoid	RTeQTL
rs11211517	CMPK1	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47780200-47798400	Weak transcription	Spleen	Spleen
2	chr1:47791800-47798200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:47792600-47798400	Weak transcription	Primary T cells from cord blood	blood
4	chr1:47792800-47798600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:47794000-47798200	Weak transcription	Ovary	ovary
6	chr1:47795200-47798200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:47795200-47798200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:47795600-47798600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:47796000-47798200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:47796200-47798200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:47796600-47798600	Enhancers	Esophagus	oesophagus
12	chr1:47797400-47798200	Enhancers	Fetal Heart	heart
13	chr1:47797400-47798400	Enhancers	Fetal Intestine Large	intestine
14	chr1:47797600-47798200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:47797600-47798200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:47797600-47798200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr1:47797600-47798200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:47797600-47798200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:47797600-47798200	Enhancers	Fetal Intestine Small	intestine
20	chr1:47797600-47799200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:47797800-47798200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:47797800-47798200	Enhancers	Psoas Muscle	Psoas
23	chr1:47797800-47798200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr1:47797800-47798200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr1:47797800-47798400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:47797800-47798400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:47797800-47798400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:47797800-47798400	Enhancers	HMEC	breast
29	chr1:47797800-47798600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:47797800-47798600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:47797800-47798600	Enhancers	Brain Anterior Caudate	brain
32	chr1:47797800-47798600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:47797800-47798600	Enhancers	Fetal Kidney	kidney
34	chr1:47797800-47798600	Enhancers	Fetal Muscle Leg	muscle
35	chr1:47797800-47798600	Enhancers	Fetal Stomach	stomach
36	chr1:47797800-47798600	Enhancers	Right Atrium	heart
37	chr1:47797800-47798800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:47797800-47798800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:47797800-47798800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr1:47797800-47799000	Flanking Active TSS	Fetal Brain Female	brain
41	chr1:47797800-47799000	Flanking Active TSS	K562	blood
42	chr1:47797800-47799200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:47797800-47799200	Enhancers	Small Intestine	intestine
44	chr1:47798000-47798200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr1:47798000-47798200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:47798000-47798200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr1:47798000-47798200	Enhancers	Brain Angular Gyrus	brain
48	chr1:47798000-47798200	Enhancers	Brain Hippocampus Middle	brain
49	chr1:47798000-47798200	Enhancers	Colonic Mucosa	Colon
50	chr1:47798000-47798200	Enhancers	Rectal Mucosa Donor 31	rectum

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