Variant report

Variant	rs2677108
Chromosome Location	chr6:45403774-45403775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:45403577..45407385-chr6:45411377..45414376,7	K562	blood:
2	chr6:45342387..45347008-chr6:45403451..45407825,6	K562	blood:
3	chr6:45375953..45377768-chr6:45403228..45404829,2	MCF-7	breast:
4	chr6:45395765..45397797-chr6:45403659..45406189,2	K562	blood:
5	chr6:45383474..45385302-chr6:45402445..45404641,2	K562	blood:
6	chr6:45347663..45349409-chr6:45402335..45404228,2	K562	blood:
7	chr6:45392117..45393805-chr6:45402414..45404150,2	MCF-7	breast:
8	chr6:45385643..45388546-chr6:45402027..45403903,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1997992	0.96[YRI][hapmap];0.97[AFR][1000 genomes]
rs2064630	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2224118	0.89[AFR][1000 genomes]
rs2677101	0.82[ASW][hapmap];0.82[CHD][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2677102	0.88[AFR][1000 genomes]
rs2819854	0.92[YRI][hapmap];0.94[AFR][1000 genomes]
rs2819857	0.89[AFR][1000 genomes]
rs2819858	0.86[AFR][1000 genomes]
rs2819859	0.87[AFR][1000 genomes]
rs9395101	0.88[AFR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2677108	SUPT3H	cis	cerebellum	SCAN
rs2677108	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL
rs2677108	SUPT3H	cis	parietal	SCAN

Chromatin state (count:61 , 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	chr6:45394400-45413200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:45396800-45404200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:45397400-45405400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:45398400-45404200	Enhancers	Primary hematopoietic stem cells	blood
7	chr6:45398600-45404200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:45398800-45403800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:45399000-45404600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:45399400-45404000	Weak transcription	HSMMtube	muscle
11	chr6:45399400-45423600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:45399800-45404400	Weak transcription	Thymus	Thymus
13	chr6:45399800-45405000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:45399800-45410600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:45400000-45404000	Genic enhancers	Osteobl	bone
16	chr6:45400000-45406600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr6:45400200-45404200	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr6:45400200-45405800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr6:45400200-45409600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:45400400-45404200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:45400800-45404200	Weak transcription	Stomach Mucosa	stomach
22	chr6:45401200-45406600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:45401400-45404000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:45401400-45404200	Weak transcription	Hela-S3	cervix
25	chr6:45401400-45407200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr6:45401600-45404200	Weak transcription	Fetal Kidney	kidney
27	chr6:45401600-45404200	Enhancers	Dnd41	blood
28	chr6:45401800-45404200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:45401800-45404400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:45402000-45403800	Weak transcription	NHDF-Ad	bronchial
31	chr6:45402000-45404000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:45402000-45404200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:45402000-45404600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:45402000-45413200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr6:45402200-45403800	Weak transcription	NHEK	skin
36	chr6:45402200-45404000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:45402200-45404000	Weak transcription	NH-A	brain
38	chr6:45402200-45404200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:45402200-45404200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:45402400-45404000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:45402400-45404000	Weak transcription	HMEC	breast
42	chr6:45402400-45404200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr6:45402600-45403800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:45402600-45404000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr6:45402600-45404000	Weak transcription	HUVEC	blood vessel
46	chr6:45402600-45404200	Weak transcription	Primary T cells from cord blood	blood
47	chr6:45402600-45404400	Weak transcription	Fetal Lung	lung
48	chr6:45402800-45403800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr6:45402800-45403800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:45402800-45404200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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