Variant report

Variant	rs1997992
Chromosome Location	chr6:45404230-45404231
allele	A/G
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	chr6:45343327..45346622-chr6:45403898..45406831,3	K562	blood:
5	chr6:45395765..45397797-chr6:45403659..45406189,2	K562	blood:
6	chr6:45383474..45385302-chr6:45402445..45404641,2	K562	blood:
7	chr6:45404085..45406503-chr6:45408205..45409935,3	K562	blood:
8	chr14:21727224..21727734-chr6:45404153..45404890,2	NB4	blood:

No data

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1406846	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];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2224118	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2677101	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2677102	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2677108	0.96[YRI][hapmap];0.97[AFR][1000 genomes]
rs2819854	1.00[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2819855	0.96[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2819857	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2819858	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2819859	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6908650	0.82[CEU][hapmap]
rs71537499	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9395101	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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
rs1997992	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 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	chr6:45397400-45405400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:45399000-45404600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:45399400-45423600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:45399800-45404400	Weak transcription	Thymus	Thymus
8	chr6:45399800-45405000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:45399800-45410600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:45400000-45406600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr6:45400200-45405800	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr6:45400200-45409600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:45401200-45406600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:45401400-45407200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:45401800-45404400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:45402000-45404600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:45402000-45413200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:45402600-45404400	Weak transcription	Fetal Lung	lung
19	chr6:45403000-45410600	Enhancers	Fetal Thymus	thymus
20	chr6:45403400-45404400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:45403400-45405000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:45403400-45405400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr6:45403400-45405600	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr6:45403400-45408400	Enhancers	K562	blood
25	chr6:45403600-45404400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr6:45403600-45404400	Enhancers	NHLF	lung
27	chr6:45403600-45404800	Enhancers	HSMM	muscle
28	chr6:45403600-45405200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:45403800-45404400	Enhancers	NHDF-Ad	bronchial
30	chr6:45403800-45404400	Enhancers	NHEK	skin
31	chr6:45403800-45404600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr6:45403800-45405400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr6:45403800-45407400	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr6:45403800-45407800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:45403800-45413200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:45404000-45404400	Enhancers	HMEC	breast
37	chr6:45404000-45404400	Enhancers	NH-A	brain
38	chr6:45404000-45405000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr6:45404000-45405400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:45404000-45405400	Enhancers	HUVEC	blood vessel
41	chr6:45404000-45406600	Enhancers	HSMMtube	muscle
42	chr6:45404000-45407600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:45404000-45408000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:45404200-45404400	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr6:45404200-45404400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:45404200-45404400	Enhancers	Fetal Intestine Large	intestine
47	chr6:45404200-45404400	Enhancers	Small Intestine	intestine
48	chr6:45404200-45404600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:45404200-45404600	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr6:45404200-45404600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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