Variant report

Variant	rs1108040
Chromosome Location	chr6:5026715-5026716
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr6:5026257-5027165	IMR90	lung:	n/a	chr6:5026724-5026733 chr6:5026616-5026626 chr6:5026596-5026606
2	MAX	chr6:5026372-5027089	K562	blood:	n/a	chr6:5026724-5026733 chr6:5026616-5026626 chr6:5026596-5026606
3	POLR2A	chr6:5026421-5026852	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:5026146-5027049	H1-hESC	embryonic stem cell:	n/a	n/a
5	USF1	chr6:5026570-5027026	HepG2	liver:	n/a	chr6:5026722-5026735 chr6:5026724-5026733 chr6:5026724-5026733 chr6:5026835-5026846 chr6:5026723-5026732 chr6:5026718-5026739
6	TAF1	chr6:5026121-5026961	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr6:5026081-5027128	H1-hESC	embryonic stem cell:	n/a	chr6:5026724-5026733 chr6:5026616-5026626 chr6:5026596-5026606
8	BACH1	chr6:5025892-5026956	H1-hESC	embryonic stem cell:	n/a	n/a
9	USF1	chr6:5026552-5026872	SK-N-SH_RA	brain:	n/a	chr6:5026722-5026735 chr6:5026724-5026733 chr6:5026724-5026733 chr6:5026835-5026846 chr6:5026723-5026732 chr6:5026718-5026739
10	TBP	chr6:5026609-5026952	K562	blood:	n/a	n/a
11	POLR2A	chr6:5026170-5026923	SK-N-MC	brain:	n/a	n/a
12	ELF1	chr6:5026610-5026902	K562	blood:	n/a	n/a
13	TAF1	chr6:5026236-5027010	H1-hESC	embryonic stem cell:	n/a	n/a
14	TBP	chr6:5025949-5027028	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr6:5026703-5027108	H1-hESC	embryonic stem cell:	n/a	chr6:5026724-5026733
16	MXI1	chr6:5026017-5027131	IMR90	lung:	n/a	chr6:5026723-5026732
17	CTCF	chr6:5026620-5026770	AG09309	skin:	n/a	n/a
18	RCOR1	chr6:5026263-5026885	K562	blood:	n/a	n/a
19	CHD2	chr6:5026708-5026800	K562	blood:	n/a	n/a
20	MAFK	chr6:5026303-5026960	K562	blood:	n/a	chr6:5026467-5026476 chr6:5026462-5026477 chr6:5026467-5026477 chr6:5026465-5026481 chr6:5026466-5026480
21	USF1	chr6:5026473-5026994	H1-hESC	embryonic stem cell:	n/a	chr6:5026722-5026735 chr6:5026724-5026733 chr6:5026724-5026733 chr6:5026835-5026846 chr6:5026723-5026732 chr6:5026718-5026739
22	BHLHE40	chr6:5026312-5026978	HepG2	liver:	n/a	chr6:5026722-5026735 chr6:5026724-5026733 chr6:5026724-5026733 chr6:5026723-5026732 chr6:5026718-5026739
23	RAD21	chr6:5026212-5026743	H1-hESC	embryonic stem cell:	n/a	chr6:5026248-5026261
24	CHD2	chr6:5026323-5026742	H1-hESC	embryonic stem cell:	n/a	chr6:5026655-5026662
25	HEY1	chr6:5026310-5026993	HepG2	liver:	n/a	chr6:5026826-5026841
26	GTF2F1	chr6:5026504-5026967	H1-hESC	embryonic stem cell:	n/a	n/a
27	E2F6	chr6:5025856-5027156	H1-hESC	embryonic stem cell:	n/a	chr6:5026655-5026662
28	MYC	chr6:5026676-5026985	K562	blood:	n/a	chr6:5026724-5026733
29	MYC	chr6:5026423-5026976	K562	blood:	n/a	chr6:5026724-5026733 chr6:5026616-5026626 chr6:5026596-5026606
30	MAFK	chr6:5026258-5026898	H1-hESC	embryonic stem cell:	n/a	chr6:5026467-5026476 chr6:5026462-5026477 chr6:5026467-5026477 chr6:5026465-5026481 chr6:5026466-5026480
31	ZBTB7A	chr6:5026464-5026726	K562	blood:	n/a	chr6:5026489-5026498
32	MXI1	chr6:5026413-5027017	H1-hESC	embryonic stem cell:	n/a	chr6:5026723-5026732
33	BACH1	chr6:5026673-5026776	K562	blood:	n/a	n/a
34	POLR2A	chr6:5026328-5026910	H1-hESC	embryonic stem cell:	n/a	n/a
35	USF1	chr6:5026412-5026989	H1-hESC	embryonic stem cell:	n/a	chr6:5026722-5026735 chr6:5026724-5026733 chr6:5026724-5026733 chr6:5026835-5026846 chr6:5026723-5026732 chr6:5026718-5026739
36	USF1	chr6:5026548-5026879	SK-N-SH_RA	brain:	n/a	chr6:5026722-5026735 chr6:5026724-5026733 chr6:5026724-5026733 chr6:5026835-5026846 chr6:5026723-5026732 chr6:5026718-5026739
37	BHLHE40	chr6:5026401-5027036	K562	blood:	n/a	chr6:5026722-5026735 chr6:5026724-5026733 chr6:5026724-5026733 chr6:5026723-5026732 chr6:5026718-5026739
38	MYC	chr6:5026236-5026888	H1-hESC	embryonic stem cell:	n/a	chr6:5026724-5026733 chr6:5026616-5026626 chr6:5026596-5026606
39	CTCF	chr6:5026640-5026790	HBMEC	blood vessel:	n/a	n/a
40	POLR2A	chr6:5026715-5026994	HepG2	liver:	n/a	n/a
41	ZNF143	chr6:5026075-5026978	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr6:5026417-5026888	HepG2	liver:	n/a	n/a
43	ZMIZ1	chr6:5026610-5026752	K562	blood:	n/a	n/a
44	USF1	chr6:5026494-5026986	ECC-1	luminal epithelium:	n/a	chr6:5026722-5026735 chr6:5026724-5026733 chr6:5026724-5026733 chr6:5026835-5026846 chr6:5026723-5026732 chr6:5026718-5026739
45	HEY1	chr6:5026232-5026878	HepG2	liver:	n/a	chr6:5026826-5026841
46	POLR2A	chr6:5026700-5026980	H1-hESC	embryonic stem cell:	n/a	n/a
47	USF1	chr6:5026558-5026913	K562	blood:	n/a	chr6:5026722-5026735 chr6:5026724-5026733 chr6:5026724-5026733 chr6:5026835-5026846 chr6:5026723-5026732 chr6:5026718-5026739
48	MAX	chr6:5026108-5027056	H1-hESC	embryonic stem cell:	n/a	chr6:5026724-5026733 chr6:5026616-5026626 chr6:5026596-5026606
49	POLR2A	chr6:5026369-5027061	HepG2	liver:	n/a	n/a
50	USF1	chr6:5026583-5026863	HepG2	liver:	n/a	chr6:5026722-5026735 chr6:5026724-5026733 chr6:5026724-5026733 chr6:5026835-5026846 chr6:5026723-5026732 chr6:5026718-5026739

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5022332..5024796-chr6:5026055..5028237,3	K562	blood:

Variant related genes	Relation type
ENSG00000272142	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1108041	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11967778	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11967814	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17139235	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1749155	0.96[ASN][1000 genomes]
rs1771868	0.96[ASN][1000 genomes]
rs2147705	0.96[ASN][1000 genomes]
rs2764128	0.96[ASN][1000 genomes]
rs2764131	0.96[ASN][1000 genomes]
rs2764133	0.96[ASN][1000 genomes]
rs2764140	0.96[ASN][1000 genomes]
rs2764144	0.86[ASN][1000 genomes]
rs2764147	0.89[ASN][1000 genomes]
rs2764150	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2764170	0.96[ASN][1000 genomes]
rs2764189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2793239	1.00[JPT][hapmap]
rs2793246	0.83[ASN][1000 genomes]
rs2793252	0.82[ASN][1000 genomes]
rs2793257	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2985677	0.96[ASN][1000 genomes]
rs4281005	0.89[ASN][1000 genomes]
rs57793325	0.85[ASN][1000 genomes]
rs62385142	0.85[ASN][1000 genomes]
rs726743	0.82[ASN][1000 genomes]
rs811259	0.82[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs877229	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9378925	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5025600-5026800	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr6:5025800-5027200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:5025800-5027200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:5026000-5026800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr6:5026000-5026800	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr6:5026000-5026800	Active TSS	Brain Cingulate Gyrus	brain
7	chr6:5026000-5026800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:5026000-5027000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
9	chr6:5026000-5027000	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr6:5026000-5027000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr6:5026000-5027000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:5026000-5027000	Flanking Active TSS	Liver	Liver
13	chr6:5026000-5027000	Active TSS	Brain Angular Gyrus	brain
14	chr6:5026000-5027000	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr6:5026000-5027000	Flanking Active TSS	NHEK	skin
16	chr6:5026000-5027000	Flanking Active TSS	Osteobl	bone
17	chr6:5026000-5027200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr6:5026000-5027200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:5026000-5027200	Active TSS	Brain Anterior Caudate	brain
20	chr6:5026000-5027200	Bivalent/Poised TSS	Fetal Brain Female	brain
21	chr6:5026000-5027200	Active TSS	Fetal Kidney	kidney
22	chr6:5026000-5027200	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr6:5026000-5027200	Active TSS	Fetal Lung	lung
24	chr6:5026000-5027200	Flanking Active TSS	Fetal Muscle Trunk	muscle
25	chr6:5026000-5027200	Flanking Active TSS	Fetal Stomach	stomach
26	chr6:5026000-5027200	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr6:5026200-5026800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:5026200-5026800	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr6:5026200-5026800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:5026200-5026800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:5026200-5026800	Active TSS	Aorta	Aorta
32	chr6:5026200-5026800	Active TSS	Esophagus	oesophagus
33	chr6:5026200-5026800	Active TSS	Fetal Intestine Large	intestine
34	chr6:5026200-5026800	Active TSS	Pancreas	Pancrea
35	chr6:5026200-5026800	Active TSS	Thymus	Thymus
36	chr6:5026200-5027000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr6:5026200-5027000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:5026200-5027000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:5026200-5027000	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr6:5026200-5027000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:5026200-5027000	Active TSS	Brain Substantia Nigra	brain
42	chr6:5026200-5027000	Flanking Active TSS	Placenta	Placenta
43	chr6:5026200-5027000	Flanking Active TSS	Fetal Thymus	thymus
44	chr6:5026200-5027000	Active TSS	Gastric	stomach
45	chr6:5026200-5027000	Active TSS	Placenta Amnion	Placenta Amnion
46	chr6:5026200-5027000	Active TSS	Psoas Muscle	Psoas
47	chr6:5026200-5027000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr6:5026200-5027000	Flanking Active TSS	HUVEC	blood vessel
49	chr6:5026200-5027000	Active TSS	NHDF-Ad	bronchial
50	chr6:5026200-5027000	Flanking Active TSS	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links