Variant report

Variant	rs2256819
Chromosome Location	chr6:45418402-45418403
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45412131..45416669-chr6:45417302..45422043,11	K562	blood:
2	chr6:45415340..45418942-chr6:45422164..45424791,5	K562	blood:
3	chr6:45416687..45419671-chr6:45507233..45509746,2	K562	blood:

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

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

rs_ID	r²[population]
rs10214519	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12197948	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12210100	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12215249	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1317777	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13208741	1.00[JPT][hapmap]
rs1343799	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934327	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2252718	0.91[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2396442	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2677098	0.91[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677099	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677100	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677109	0.82[CEU][hapmap];0.93[EUR][1000 genomes]
rs2677110	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790093	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790094	0.91[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2790095	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2790097	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2790098	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790099	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790100	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790102	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs2790103	0.91[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2819852	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819853	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819861	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]
rs2819864	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819865	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819866	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2819867	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820339	0.91[CEU][hapmap];0.98[EUR][1000 genomes]
rs2820340	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711816	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs4714854	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6458443	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765724	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7756144	0.90[EUR][1000 genomes]
rs910586	0.91[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9472494	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9885645	0.91[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[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
rs2256819	RUNX2	cis	multi-tissue	Pritchard

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45399400-45423600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:45407200-45462000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:45413400-45423400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:45414000-45421400	Weak transcription	Esophagus	oesophagus
5	chr6:45414000-45431400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:45414200-45419000	Enhancers	K562	blood
7	chr6:45414400-45420000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:45415000-45421000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:45415000-45421800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:45415200-45421800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:45415200-45421800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:45415200-45422200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:45415200-45422200	Weak transcription	HMEC	breast
14	chr6:45415600-45419200	Enhancers	Fetal Thymus	thymus
15	chr6:45415600-45424600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:45415800-45419000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr6:45415800-45420000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr6:45415800-45421800	Weak transcription	NHEK	skin
19	chr6:45416000-45420800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr6:45416000-45421800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:45416200-45420000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:45416200-45421800	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr6:45416400-45419400	Weak transcription	Colonic Mucosa	Colon
24	chr6:45416400-45421200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:45416400-45421200	Weak transcription	HUVEC	blood vessel
26	chr6:45416400-45421800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:45416400-45430600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:45416400-45440400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:45416600-45430000	Weak transcription	Small Intestine	intestine
30	chr6:45416800-45418600	Strong transcription	Primary hematopoietic stem cells	blood
31	chr6:45416800-45420600	Strong transcription	NH-A	brain
32	chr6:45417200-45419400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr6:45417200-45419400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:45417200-45419800	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr6:45417200-45421200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr6:45417200-45421400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr6:45417200-45422400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:45417400-45419000	Strong transcription	HSMM	muscle
39	chr6:45417400-45419800	Enhancers	Dnd41	blood
40	chr6:45417400-45419800	Weak transcription	Hela-S3	cervix
41	chr6:45417400-45420600	Weak transcription	NHDF-Ad	bronchial
42	chr6:45417400-45420800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:45417400-45421200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:45417400-45421400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:45417400-45421400	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr6:45417400-45421800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr6:45417600-45418800	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr6:45417600-45419200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:45417600-45421200	Strong transcription	Osteobl	bone
50	chr6:45417600-45422200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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