Variant report

Variant	rs1057407
Chromosome Location	chr8:57906313-57906314
allele	C/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	BACH1	chr8:57905485-57907050	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr8:57906241-57906546	HepG2	liver:	n/a	n/a
3	NR2C2	chr8:57905556-57906676	Hela-S3	cervix:	n/a	chr8:57906420-57906435
4	TAF1	chr8:57906204-57906741	SK-N-SH	brain:	n/a	n/a
5	TAF1	chr8:57906238-57906710	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr8:57906223-57906674	A549	lung:	n/a	n/a
7	MAX	chr8:57905382-57907110	Hela-S3	cervix:	n/a	n/a
8	MYC	chr8:57905491-57906639	MCF-7	breast:	n/a	n/a
9	EGR1	chr8:57906048-57907075	HCT-116	colon:	n/a	chr8:57906433-57906446 chr8:57906798-57906807 chr8:57906434-57906445 chr8:57906864-57906871 chr8:57906436-57906445 chr8:57906435-57906445 chr8:57906433-57906447 chr8:57906435-57906445
10	JUND	chr8:57906217-57906652	A549	lung:	n/a	chr8:57906259-57906268 chr8:57906333-57906342
11	MAX	chr8:57906212-57906585	NB4	blood:	n/a	n/a
12	EGR1	chr8:57906271-57906650	H1-hESC	embryonic stem cell:	n/a	chr8:57906433-57906446 chr8:57906434-57906445 chr8:57906436-57906445 chr8:57906435-57906445 chr8:57906433-57906447 chr8:57906435-57906445
13	MYC	chr8:57906289-57906449	HUVEC	blood vessel:	n/a	n/a
14	YY1	chr8:57906205-57906480	GM12878	blood:	n/a	chr8:57906263-57906274
15	SIN3AK20	chr8:57906233-57906925	PFSK-1	brain:	n/a	n/a
16	FOXP2	chr8:57906178-57906491	SK-N-MC	brain:	n/a	n/a
17	TBP	chr8:57906240-57906776	H1-hESC	embryonic stem cell:	n/a	n/a
18	GABPA	chr8:57906256-57906518	HepG2	liver:	n/a	chr8:57906337-57906346
19	POLR2A	chr8:57906234-57906616	K562	blood:	n/a	n/a
20	MAZ	chr8:57906263-57906571	GM12878	blood:	n/a	n/a
21	EGR1	chr8:57906212-57907045	HCT-116	colon:	n/a	chr8:57906433-57906446 chr8:57906798-57906807 chr8:57906434-57906445 chr8:57906864-57906871 chr8:57906436-57906445 chr8:57906435-57906445 chr8:57906433-57906447 chr8:57906435-57906445
22	YY1	chr8:57906260-57906461	A549	lung:	n/a	chr8:57906263-57906274
23	MAX	chr8:57905377-57906717	K562	blood:	n/a	n/a
24	POLR2A	chr8:57905255-57906979	IMR90	lung:	n/a	n/a
25	POLR2A	chr8:57905909-57906849	H1-hESC	embryonic stem cell:	n/a	n/a
26	PAX5	chr8:57905880-57906589	GM12892	blood:	n/a	n/a
27	REST	chr8:57906261-57906656	HepG2	liver:	n/a	chr8:57906266-57906279
28	ELF1	chr8:57906077-57906809	MCF-7	breast:	n/a	n/a
29	POLR2A	chr8:57906246-57906609	K562	blood:	n/a	n/a
30	POLR2A	chr8:57906218-57906682	HL-60	blood:	n/a	n/a
31	POLR2A	chr8:57906240-57906490	HepG2	liver:	n/a	n/a
32	EP300	chr8:57906086-57906743	ECC-1	luminal epithelium:	n/a	chr8:57906156-57906172 chr8:57906260-57906276 chr8:57906267-57906283
33	GABPA	chr8:57906242-57906526	GM12878	blood:	n/a	chr8:57906337-57906346
34	GTF2F1	chr8:57906304-57906411	K562	blood:	n/a	n/a
35	RCOR1	chr8:57906305-57906402	HepG2	liver:	n/a	n/a
36	HDAC2	chr8:57906214-57906484	K562	blood:	n/a	n/a
37	POLR2A	chr8:57906224-57906504	GM12891	blood:	n/a	n/a
38	SIN3AK20	chr8:57906257-57906500	HepG2	liver:	n/a	n/a
39	POLR2A	chr8:57905786-57906886	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr8:57905409-57907614	MCF10A-Er-Src	breast:	n/a	n/a
41	GABPA	chr8:57906303-57906477	Hela-S3	cervix:	n/a	chr8:57906337-57906346
42	CEBPB	chr8:57906275-57906900	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr8:57906236-57906811	HCT-116	colon:	n/a	n/a
44	POLR2A	chr8:57905533-57906892	A549	lung:	n/a	n/a
45	POLR2A	chr8:57905577-57906824	ProgFib	skin:	n/a	n/a
46	MAX	chr8:57905337-57906791	HepG2	liver:	n/a	n/a
47	ELF1	chr8:57906210-57906626	HepG2	liver:	n/a	n/a
48	POLR2A	chr8:57906234-57906839	SK-N-MC	brain:	n/a	n/a
49	FOSL2	chr8:57906245-57906504	HepG2	liver:	n/a	chr8:57906259-57906268 chr8:57906333-57906342
50	TBL1XR1	chr8:57906284-57906642	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:57891643..57894816-chr8:57903794..57907010,5	K562	blood:
2	chr8:57892210..57896083-chr8:57903794..57907547,6	K562	blood:
3	chr8:57891263..57893548-chr8:57905444..57907032,2	MCF-7	breast:

Variant related genes	Relation type
IMPAD1	TF binding region
ENSG00000104331	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1046636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1046643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12679713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13256360	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13257046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13265996	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13272145	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13278306	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13278878	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35400916	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3739364	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56922495	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62511999	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62512025	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71519474	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs925150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029443	chr8:57748114-58057656	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv3430321	chr8:57858417-58055129	Strong transcription Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1027125	chr8:57891279-58095884	Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv3436028	chr8:57905223-57907771	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:57901800-57907200	Active TSS	GM12878-XiMat	blood
2	chr8:57903200-57907000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr8:57903400-57907200	Active TSS	Psoas Muscle	Psoas
4	chr8:57903600-57906800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:57903600-57907200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr8:57903600-57907200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr8:57903800-57907200	Active TSS	NHDF-Ad	bronchial
8	chr8:57904000-57906600	Active TSS	K562	blood
9	chr8:57904000-57907000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr8:57904000-57907000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr8:57904000-57907200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr8:57904000-57907400	Active TSS	HMEC	breast
13	chr8:57904200-57907200	Active TSS	Right Atrium	heart
14	chr8:57904200-57907400	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr8:57904400-57906800	Active TSS	Brain Angular Gyrus	brain
16	chr8:57904400-57907200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr8:57904400-57907200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr8:57904400-57907200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr8:57904400-57907200	Active TSS	HSMMtube	muscle
20	chr8:57904400-57907400	Active TSS	NHLF	lung
21	chr8:57904600-57906800	Active TSS	Fetal Muscle Leg	muscle
22	chr8:57904600-57907000	Active TSS	Placenta	Placenta
23	chr8:57904600-57907000	Active TSS	Fetal Stomach	stomach
24	chr8:57904600-57907200	Active TSS	Ovary	ovary
25	chr8:57904600-57907200	Active TSS	Right Ventricle	heart
26	chr8:57904600-57907200	Active TSS	Thymus	Thymus
27	chr8:57904600-57907200	Active TSS	HSMM	muscle
28	chr8:57904800-57906600	Active TSS	Fetal Thymus	thymus
29	chr8:57904800-57907000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr8:57904800-57907000	Active TSS	Brain Germinal Matrix	brain
31	chr8:57904800-57907000	Active TSS	A549	lung
32	chr8:57904800-57907000	Active TSS	Hela-S3	cervix
33	chr8:57904800-57907200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr8:57904800-57907200	Active TSS	Colonic Mucosa	Colon
35	chr8:57904800-57907200	Active TSS	NHEK	skin
36	chr8:57904800-57907400	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr8:57905000-57906400	Active TSS	Small Intestine	intestine
38	chr8:57905000-57906600	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr8:57905000-57906600	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr8:57905000-57906800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr8:57905000-57906800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr8:57905000-57906800	Active TSS	Brain Substantia Nigra	brain
43	chr8:57905000-57906800	Active TSS	Fetal Brain Male	brain
44	chr8:57905000-57906800	Active TSS	Fetal Brain Female	brain
45	chr8:57905000-57906800	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr8:57905000-57906800	Active TSS	HUVEC	blood vessel
47	chr8:57905000-57906800	Active TSS	NH-A	brain
48	chr8:57905000-57906800	Active TSS	Osteobl	bone
49	chr8:57905000-57907000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr8:57905000-57907000	Active TSS	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links