Variant report

Variant	rs2819861
Chromosome Location	chr6:45424940-45424941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45419545..45421577-chr6:45423010..45426161,3	MCF-7	breast:
2	chr6:45423983..45426687-chr6:45430740..45433048,2	MCF-7	breast:
3	chr6:45416242..45417772-chr6:45424221..45426161,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10214519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12197948	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12210100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12215249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1317777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13208741	1.00[JPT][hapmap]
rs1343799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934327	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2252718	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2256819	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396442	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2677098	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677099	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677100	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677109	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2677110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790094	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2790095	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2790097	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2790098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790099	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790102	1.00[CEU][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs2790103	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2819852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819865	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819866	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2819867	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820339	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs2820340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711816	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4714854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6458443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7756144	0.89[EUR][1000 genomes]
rs910586	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9472494	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9885645	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2819861	MRPL2	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45407200-45462000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:45414000-45431400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:45416400-45430600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:45416400-45440400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:45416600-45430000	Weak transcription	Small Intestine	intestine
6	chr6:45418200-45427400	Weak transcription	Aorta	Aorta
7	chr6:45419200-45456200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr6:45419400-45429000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr6:45420000-45425200	Strong transcription	Dnd41	blood
10	chr6:45420800-45425600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr6:45421200-45428800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr6:45422000-45425200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:45422000-45425400	Weak transcription	Fetal Thymus	thymus
14	chr6:45422000-45428800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:45422000-45429000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:45422000-45429000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:45422000-45441200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:45422000-45445000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:45422200-45440000	Weak transcription	Brain Angular Gyrus	brain
20	chr6:45422400-45425200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:45422400-45427800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr6:45422400-45428800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr6:45422400-45429000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:45422400-45438200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr6:45422600-45425000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:45422600-45428000	Weak transcription	HSMMtube	muscle
27	chr6:45422600-45429200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:45422600-45432400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:45422600-45437200	Weak transcription	NHDF-Ad	bronchial
30	chr6:45422600-45439800	Weak transcription	NHLF	lung
31	chr6:45422800-45428800	Strong transcription	HSMM	muscle
32	chr6:45423000-45425600	Strong transcription	Osteobl	bone
33	chr6:45423000-45428200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:45423000-45454400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:45423200-45425200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:45423400-45425000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:45423400-45426600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:45423400-45428800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:45423400-45434600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:45423600-45429200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr6:45423800-45429200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:45424000-45425200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:45424000-45425400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:45424200-45425000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:45424200-45425200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:45424200-45425200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr6:45424200-45425600	Strong transcription	NH-A	brain
48	chr6:45424200-45429000	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr6:45424600-45425400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:45424600-45429200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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