Variant report

Variant	rs3828722
Chromosome Location	chr6:45392982-45392983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45346603..45348483-chr6:45391933..45394862,2	K562	blood:
2	chr6:45391180..45393282-chr6:45393319..45396759,3	K562	blood:
3	chr6:45391466..45393363-chr6:45413859..45416202,2	MCF-7	breast:
4	chr6:45369759..45372221-chr6:45390852..45393677,2	K562	blood:
5	chr6:45392117..45393805-chr6:45402414..45404150,2	MCF-7	breast:
6	chr6:45391736..45393950-chr6:45394810..45397600,3	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1004130	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10498760	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11498195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963804	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11966462	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11968177	0.82[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs17209846	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17209853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17209874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17209881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17288355	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17288376	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17288390	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs17288397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3749864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805811	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4370348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413613	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56789892	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57013196	0.80[ASN][1000 genomes]
rs58571027	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59397804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61467394	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6921145	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7768466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771980	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296459	0.90[JPT][hapmap]

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

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45388400-45393400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:45388600-45393000	Active TSS	NHLF	lung
3	chr6:45390800-45393000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr6:45391000-45393000	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr6:45391200-45393200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
6	chr6:45391400-45393400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:45391600-45394400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:45392200-45394200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:45392200-45394400	Flanking Active TSS	Osteobl	bone
10	chr6:45392200-45395000	Enhancers	Dnd41	blood
11	chr6:45392200-45396400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr6:45392200-45400600	Weak transcription	HMEC	breast
13	chr6:45392200-45404800	Weak transcription	Brain Substantia Nigra	brain
14	chr6:45392400-45393400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:45392400-45393400	Active TSS	Duodenum Mucosa	Duodenum
16	chr6:45392400-45394000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:45392400-45394200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:45392400-45396000	Enhancers	NHDF-Ad	bronchial
19	chr6:45392400-45398200	Weak transcription	HSMMtube	muscle
20	chr6:45392400-45398600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:45392400-45400000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:45392400-45400600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:45392400-45406800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:45392600-45393000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:45392600-45393000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:45392600-45393000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:45392600-45393000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr6:45392600-45393400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:45392600-45393400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:45392600-45393400	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr6:45392600-45393400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:45392600-45395800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:45392600-45400600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:45392800-45393000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:45392800-45393000	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr6:45392800-45393000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr6:45392800-45393000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr6:45392800-45393000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:45392800-45393000	Enhancers	HSMM	muscle
40	chr6:45392800-45393200	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr6:45392800-45393200	Flanking Active TSS	NH-A	brain
42	chr6:45392800-45399000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:45392800-45399200	Weak transcription	Primary T cells fromperipheralblood	blood

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