Variant report

Variant	rs2859141
Chromosome Location	chr6:36099760-36099761
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36086127..36086828-chr6:36099610..36100336,2	MCF-7	breast:
2	chr6:36099611..36101703-chr6:36163154..36166410,4	K562	blood:
3	chr6:36097672..36103046-chr6:36163327..36166048,5	MCF-7	breast:
4	chr6:36099568..36102831-chr6:36104693..36107135,4	MCF-7	breast:
5	chr6:36084320..36086467-chr6:36099428..36101090,2	MCF-7	breast:
6	chr6:36098131..36102554-chr6:36163258..36166179,4	K562	blood:

Variant related genes	Relation type
ENSG00000096070	Chromatin interaction
ENSG00000246982	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10447375	0.85[AMR][1000 genomes]
rs10447396	0.93[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1059227	0.93[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947589	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12193895	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12199702	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12201042	0.81[AMR][1000 genomes]
rs12201072	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12210904	0.87[AMR][1000 genomes]
rs12210946	0.83[ASN][1000 genomes]
rs12525283	1.00[JPT][hapmap]
rs17715809	1.00[JPT][hapmap]
rs2007683	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859135	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2859136	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2859137	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4711433	0.86[AMR][1000 genomes]
rs6940723	0.81[AMR][1000 genomes];0.96[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	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2859141	RP1-179N16.6	cis	Whole Blood	GTEx
rs2859141	MAPK13	cis	Esophagus Mucosa	GTEx
rs2859141	MAPK13	Cis_1M	lymphoblastoid	RTeQTL
rs2859141	MAPK13	cis	multi-tissue	Pritchard
rs2859141	SCUBE3	cis	cerebellum	SCAN
rs2859141	CLPS	cis	parietal	SCAN
rs2859141	KIF6	cis	cerebellum	SCAN
rs2859141	MAPK13	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36097400-36099800	Enhancers	HUVEC	blood vessel
2	chr6:36097600-36099800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr6:36097600-36100200	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr6:36097600-36101000	Enhancers	Fetal Heart	heart
5	chr6:36098200-36100200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr6:36098200-36100600	Enhancers	NHLF	lung
7	chr6:36098200-36107000	Weak transcription	HSMMtube	muscle
8	chr6:36098400-36099800	Flanking Active TSS	NHDF-Ad	bronchial
9	chr6:36098400-36100200	Flanking Active TSS	GM12878-XiMat	blood
10	chr6:36098400-36100400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:36098400-36100600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:36098600-36099800	Flanking Active TSS	Pancreas	Pancrea
13	chr6:36098600-36099800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
14	chr6:36098600-36099800	Flanking Active TSS	NHEK	skin
15	chr6:36098600-36100000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:36098600-36100000	Flanking Active TSS	Primary B cells from peripheral blood	blood
17	chr6:36098600-36100000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:36098600-36100000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:36098600-36100000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr6:36098600-36100200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr6:36098600-36100200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr6:36098600-36100400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr6:36098600-36100400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:36098600-36100400	Flanking Active TSS	Colonic Mucosa	Colon
25	chr6:36098600-36100400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr6:36098600-36100800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:36098800-36099800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:36098800-36099800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:36098800-36099800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr6:36098800-36099800	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr6:36098800-36099800	Enhancers	NH-A	brain
32	chr6:36098800-36100200	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr6:36098800-36100200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr6:36098800-36100200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:36098800-36100200	Flanking Active TSS	HepG2	liver
36	chr6:36098800-36100400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr6:36098800-36100600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr6:36098800-36100600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:36098800-36101000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:36099000-36099800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr6:36099000-36099800	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr6:36099000-36099800	Active TSS	Esophagus	oesophagus
43	chr6:36099000-36100000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr6:36099000-36100000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:36099000-36100000	Enhancers	Left Ventricle	heart
46	chr6:36099000-36100200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:36099000-36100200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:36099000-36100400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:36099000-36100400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr6:36099000-36100600	Enhancers	Spleen	Spleen

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