Variant report

Variant	rs2819855
Chromosome Location	chr6:45400394-45400395
allele	C/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: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10948234	0.81[CEU][hapmap]
rs1406846	0.82[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17288390	0.81[CEU][hapmap]
rs1997992	0.96[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2064630	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2224118	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2677101	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[ASN][1000 genomes]
rs2677102	1.00[ASN][1000 genomes]
rs2819857	1.00[ASN][1000 genomes]
rs2819858	1.00[ASN][1000 genomes]
rs2819859	1.00[ASN][1000 genomes]
rs71537499	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7770471	0.91[CEU][hapmap]
rs9296459	0.81[CEU][hapmap];0.86[GIH][hapmap]
rs9395101	1.00[ASN][1000 genomes]
rs9472487	0.87[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
rs2819855	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45392200-45400600	Weak transcription	HMEC	breast
2	chr6:45392200-45404800	Weak transcription	Brain Substantia Nigra	brain
3	chr6:45392400-45400600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:45392400-45406800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:45392600-45400600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:45393000-45400600	Weak transcription	NHLF	lung
7	chr6:45394400-45401600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:45394400-45413200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:45396000-45400400	Weak transcription	NHDF-Ad	bronchial
10	chr6:45396400-45400400	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr6:45396400-45401400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr6:45396800-45404200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:45397400-45405400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:45397800-45402400	Genic enhancers	HSMM	muscle
15	chr6:45397800-45402800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr6:45398000-45401600	Genic enhancers	Dnd41	blood
17	chr6:45398200-45400400	Strong transcription	NH-A	brain
18	chr6:45398200-45401000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:45398400-45402600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr6:45398400-45404200	Enhancers	Primary hematopoietic stem cells	blood
21	chr6:45398600-45402600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr6:45398600-45404200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:45398800-45403800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:45399000-45400600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:45399000-45404600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:45399400-45400800	Weak transcription	K562	blood
27	chr6:45399400-45403400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr6:45399400-45404000	Weak transcription	HSMMtube	muscle
29	chr6:45399400-45423600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:45399600-45400600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:45399600-45400800	Weak transcription	Primary T cells from cord blood	blood
32	chr6:45399800-45400400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:45399800-45400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:45399800-45400600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:45399800-45400800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:45399800-45401600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:45399800-45401600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:45399800-45401600	Weak transcription	Fetal Thymus	thymus
39	chr6:45399800-45403200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr6:45399800-45404400	Weak transcription	Thymus	Thymus
41	chr6:45399800-45405000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:45399800-45410600	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr6:45400000-45400400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr6:45400000-45402600	Enhancers	HUVEC	blood vessel
45	chr6:45400000-45403000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:45400000-45404000	Genic enhancers	Osteobl	bone
47	chr6:45400000-45406600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr6:45400200-45400600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:45400200-45401000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:45400200-45401800	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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