Variant report

Variant	rs1406846
Chromosome Location	chr6:45400940-45400941
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45389973..45394280-chr6:45398932..45403066,5	MCF-7	breast:
2	chr6:45395577..45398592-chr6:45399582..45403433,4	K562	blood:
3	chr6:45395052..45396877-chr6:45399435..45401703,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124813	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1997992	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2064630	0.83[CHB][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2224118	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2677101	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2677102	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819854	0.96[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2819855	0.82[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2819857	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819858	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819859	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6908650	0.85[CEU][hapmap]
rs71537499	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9395101	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9472487	0.83[CHB][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1406846	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45392200-45404800	Weak transcription	Brain Substantia Nigra	brain
2	chr6:45392400-45406800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:45394400-45401600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:45394400-45413200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:45396400-45401400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr6:45396800-45404200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:45397400-45405400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:45397800-45402400	Genic enhancers	HSMM	muscle
9	chr6:45397800-45402800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr6:45398000-45401600	Genic enhancers	Dnd41	blood
11	chr6:45398200-45401000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:45398400-45402600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr6:45398400-45404200	Enhancers	Primary hematopoietic stem cells	blood
14	chr6:45398600-45402600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr6:45398600-45404200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:45398800-45403800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:45399000-45404600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:45399400-45403400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr6:45399400-45404000	Weak transcription	HSMMtube	muscle
20	chr6:45399400-45423600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:45399800-45401600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:45399800-45401600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:45399800-45401600	Weak transcription	Fetal Thymus	thymus
24	chr6:45399800-45403200	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr6:45399800-45404400	Weak transcription	Thymus	Thymus
26	chr6:45399800-45405000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:45399800-45410600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr6:45400000-45402600	Enhancers	HUVEC	blood vessel
29	chr6:45400000-45403000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:45400000-45404000	Genic enhancers	Osteobl	bone
31	chr6:45400000-45406600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr6:45400200-45401000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:45400200-45401800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr6:45400200-45404200	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr6:45400200-45405800	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr6:45400200-45409600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:45400400-45402000	Enhancers	NHDF-Ad	bronchial
38	chr6:45400400-45402200	Enhancers	NHEK	skin
39	chr6:45400400-45402400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr6:45400400-45402600	Enhancers	Fetal Lung	lung
41	chr6:45400400-45403600	Genic enhancers	Muscle Satellite Cultured Cells	--
42	chr6:45400400-45404200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:45400600-45401000	Enhancers	NH-A	brain
44	chr6:45400600-45401200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:45400600-45401400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:45400600-45401400	Enhancers	Hela-S3	cervix
47	chr6:45400600-45402200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:45400600-45402200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:45400600-45402200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:45400600-45402200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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