Variant report

Variant	rs6537560
Chromosome Location	chr10:49541419-49541420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:49540878..49543802-chr10:49546206..49547724,2	K562	blood:
2	chr10:49540944..49543155-chr10:49549106..49551548,2	MCF-7	breast:
3	chr10:49517538..49519332-chr10:49540338..49542175,2	MCF-7	breast:
4	chr10:49530623..49533140-chr10:49541361..49542874,2	MCF-7	breast:
5	chr10:49538148..49542508-chr10:49545021..49547777,3	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10218874	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10437448	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10508903	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1051507	0.92[EUR][1000 genomes]
rs1051508	0.91[EUR][1000 genomes]
rs1051509	0.88[EUR][1000 genomes]
rs10745266	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10745269	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10745270	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10776595	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10776596	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10776598	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10776600	0.82[EUR][1000 genomes]
rs10857560	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10857562	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10857566	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11101290	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11101298	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11101306	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11101317	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11101318	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11101320	0.94[EUR][1000 genomes]
rs11598434	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12411830	0.81[ASN][1000 genomes]
rs1345103	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1919708	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1919712	0.95[ASN][1000 genomes]
rs1919713	0.85[ASN][1000 genomes]
rs2263102	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2289805	0.83[ASN][1000 genomes]
rs2377351	0.80[EUR][1000 genomes]
rs2463960	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2590381	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2698761	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2698766	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2698767	0.93[ASN][1000 genomes]
rs2921271	0.83[ASN][1000 genomes]
rs3789320	0.90[EUR][1000 genomes]
rs3827680	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3827681	0.81[EUR][1000 genomes]
rs3950310	0.90[ASN][1000 genomes]
rs4838590	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61840543	0.88[ASN][1000 genomes]
rs6537561	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7072515	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7075976	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7076214	0.85[ASN][1000 genomes]
rs7086070	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7086275	0.94[EUR][1000 genomes]
rs7101060	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs734371	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7904142	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7912697	0.86[ASN][1000 genomes]
rs7924070	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8428	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs867631	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs883604	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9888128	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
6	nsv6587	chr10:49526329-49571804	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv947976	chr10:49537663-49541857	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6537560	MAPK8	Cis_1M	lymphoblastoid	RTeQTL
rs6537560	MAPK8	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49516400-49547200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr10:49516400-49559600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr10:49517800-49544600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr10:49518200-49542200	Weak transcription	HSMM	muscle
5	chr10:49518800-49542000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr10:49518800-49544000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr10:49520200-49549800	Weak transcription	HUVEC	blood vessel
8	chr10:49522800-49550800	Weak transcription	Small Intestine	intestine
9	chr10:49525000-49541600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr10:49525800-49551800	Weak transcription	Adipose Nuclei	Adipose
11	chr10:49526200-49552000	Weak transcription	NH-A	brain
12	chr10:49529000-49550800	Weak transcription	K562	blood
13	chr10:49530800-49554600	Weak transcription	Fetal Brain Male	brain
14	chr10:49535000-49541800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr10:49535400-49548200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr10:49536800-49541800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:49536800-49545200	Weak transcription	Brain Angular Gyrus	brain
18	chr10:49537400-49541800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr10:49538400-49541600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr10:49538400-49543200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
21	chr10:49538400-49543200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr10:49538600-49541800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
23	chr10:49538600-49542200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:49538600-49542800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr10:49538600-49542800	ZNF genes & repeats	Brain Germinal Matrix	brain
26	chr10:49538600-49543000	ZNF genes & repeats	Fetal Stomach	stomach
27	chr10:49538600-49545400	Weak transcription	Hela-S3	cervix
28	chr10:49538600-49551400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr10:49538800-49541800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
30	chr10:49538800-49542800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr10:49538800-49543000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr10:49538800-49544600	Weak transcription	Spleen	Spleen
33	chr10:49538800-49546600	Weak transcription	HSMMtube	muscle
34	chr10:49538800-49551200	Weak transcription	Brain Substantia Nigra	brain
35	chr10:49538800-49551400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr10:49539000-49542800	ZNF genes & repeats	Fetal Brain Female	brain
37	chr10:49539000-49551800	Weak transcription	NHLF	lung
38	chr10:49539200-49542800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr10:49539200-49555000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:49539400-49541800	Weak transcription	Thymus	Thymus
41	chr10:49539400-49542000	ZNF genes & repeats	Fetal Thymus	thymus
42	chr10:49539400-49542200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr10:49539400-49542400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr10:49539400-49548200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr10:49539600-49543000	Strong transcription	Primary T cells from cord blood	blood
46	chr10:49539600-49553400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr10:49539800-49541600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr10:49539800-49541800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr10:49539800-49541800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr10:49539800-49542000	Weak transcription	Psoas Muscle	Psoas

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