Variant report

Variant	rs11787499
Chromosome Location	chr8:52812895-52812896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:52810595-52813244	GM19099	blood:	n/a	n/a
2	POLR2A	chr8:52810298-52812957	GM18951	blood:	n/a	n/a
3	POLR2A	chr8:52810460-52813304	GM18505	blood:	n/a	n/a
4	POLR2A	chr8:52810151-52812914	Hela-S3	cervix:	n/a	n/a
5	RCOR1	chr8:52812568-52813167	GM12878	blood:	n/a	n/a
6	PML	chr8:52810212-52813305	GM12878	blood:	n/a	n/a
7	POLR2A	chr8:52811403-52812963	HUVEC	blood vessel:	n/a	n/a
8	ZNF384	chr8:52811810-52813148	K562	blood:	n/a	n/a
9	MTA3	chr8:52810360-52813108	GM12878	blood:	n/a	n/a
10	POLR2A	chr8:52809769-52815334	GM12891	blood:	n/a	n/a
11	POLR2A	chr8:52810457-52813236	Raji	blood:	n/a	n/a
12	TBP	chr8:52811393-52813010	K562	blood:	n/a	n/a
13	POLR2A	chr8:52810750-52812923	HL-60	blood:	n/a	n/a
14	MYC	chr8:52810301-52813052	NB4	blood:	n/a	chr8:52811172-52811182
15	POLR2A	chr8:52808975-52813855	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr8:52810589-52812949	HUVEC	blood vessel:	n/a	n/a
17	NFIC	chr8:52812579-52813128	GM12878	blood:	n/a	n/a
18	POLR2A	chr8:52811040-52813115	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr8:52810703-52813033	GM12892	blood:	n/a	n/a
20	MXI1	chr8:52809530-52813810	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr8:52809706-52813401	GM12878	blood:	n/a	n/a
22	IRF1	chr8:52812683-52812992	K562	blood:	n/a	chr8:52812949-52812963 chr8:52812951-52812963
23	MXI1	chr8:52811383-52812934	GM12878	blood:	n/a	n/a
24	POLR2A	chr8:52810745-52813327	K562	blood:	n/a	n/a
25	POLR2A	chr8:52810482-52813690	K562	blood:	n/a	n/a
26	RUNX3	chr8:52812517-52813075	GM12878	blood:	n/a	n/a
27	POLR2A	chr8:52810711-52812903	GM18526	blood:	n/a	n/a
28	POLR2A	chr8:52811118-52813188	HepG2	liver:	n/a	n/a
29	ZNF384	chr8:52812450-52813014	GM12878	blood:	n/a	n/a
30	TBP	chr8:52811543-52813346	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr8:52810283-52813308	SK-N-MC	brain:	n/a	n/a
32	MYC	chr8:52811426-52813058	K562	blood:	n/a	n/a
33	MYC	chr8:52811479-52812906	K562	blood:	n/a	n/a
34	MYC	chr8:52812525-52813440	MCF10A-Er-Src	breast:	n/a	n/a
35	MAX	chr8:52810160-52813088	NB4	blood:	n/a	chr8:52811172-52811182
36	RELA	chr8:52811452-52812895	GM18951	blood:	n/a	n/a
37	POLR2A	chr8:52809542-52813371	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr8:52810214-52813153	PBDE	blood:	n/a	n/a
39	FOS	chr8:52812552-52813311	HUVEC	blood vessel:	n/a	n/a
40	SPI1	chr8:52812595-52812945	HL-60	blood:	n/a	n/a
41	CHD1	chr8:52810391-52813306	GM12878	blood:	n/a	n/a
42	POLR2A	chr8:52810634-52812896	GM12892	blood:	n/a	n/a
43	POLR2A	chr8:52810500-52813381	HepG2	liver:	n/a	n/a
44	POLR2A	chr8:52808962-52813736	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:52811334..52814143-chr8:52920449..52922864,2	MCF-7	breast:
2	chr8:52811463..52813634-chr8:52919548..52922718,3	MCF-7	breast:
3	chr8:52812423..52815301-chr8:52851311..52852842,2	K562	blood:

No data

Variant related genes	Relation type
PCMTD1	TF binding region
ENSG00000253475	TF binding region
ENSG00000254136	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10086425	0.86[JPT][hapmap]
rs10086504	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs10101163	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10105030	0.86[JPT][hapmap]
rs1013621	0.86[JPT][hapmap]
rs1013622	0.86[JPT][hapmap]
rs10958304	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10958305	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs11774370	0.86[JPT][hapmap]
rs11775611	0.82[EUR][1000 genomes]
rs12335014	0.86[JPT][hapmap]
rs12681734	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs13265006	0.80[EUR][1000 genomes]
rs1517306	0.86[JPT][hapmap]
rs16916858	0.85[JPT][hapmap]
rs16916952	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16916966	0.97[YRI][hapmap]
rs2176121	0.86[JPT][hapmap]
rs34058697	0.81[EUR][1000 genomes]
rs34372756	0.82[EUR][1000 genomes]
rs35032384	0.80[EUR][1000 genomes]
rs4242479	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4565453	0.86[JPT][hapmap]
rs6473660	0.86[JPT][hapmap]
rs6986544	0.86[JPT][hapmap]
rs71513561	0.81[EUR][1000 genomes]
rs7462096	0.86[JPT][hapmap]
rs7814421	0.86[JPT][hapmap]
rs925762	0.86[JPT][hapmap]
rs9298462	0.86[JPT][hapmap]
rs9650179	0.82[EUR][1000 genomes]
rs9650180	0.81[EUR][1000 genomes]
rs9650305	0.82[EUR][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	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv831316	chr8:52660353-52842928	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52809000-52813000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr8:52809000-52813200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr8:52809000-52813400	Active TSS	Ovary	ovary
4	chr8:52809000-52814000	Active TSS	GM12878-XiMat	blood
5	chr8:52809200-52813000	Active TSS	H1 Cell Line	embryonic stem cell
6	chr8:52809200-52813000	Active TSS	Stomach Smooth Muscle	stomach
7	chr8:52809200-52814000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr8:52809400-52813000	Active TSS	Fetal Muscle Leg	muscle
9	chr8:52809400-52813000	Active TSS	Fetal Stomach	stomach
10	chr8:52809600-52813000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr8:52809600-52813000	Active TSS	Fetal Intestine Large	intestine
12	chr8:52809600-52813000	Active TSS	Right Ventricle	heart
13	chr8:52809600-52813000	Active TSS	NHDF-Ad	bronchial
14	chr8:52809600-52813200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr8:52809600-52813200	Active TSS	Right Atrium	heart
16	chr8:52809600-52813400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr8:52809600-52813400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr8:52809600-52813400	Active TSS	HSMM	muscle
19	chr8:52809600-52813600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr8:52809600-52813600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr8:52809800-52813000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr8:52809800-52813000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr8:52809800-52813000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr8:52809800-52813000	Active TSS	Thymus	Thymus
25	chr8:52809800-52813000	Active TSS	HMEC	breast
26	chr8:52809800-52813000	Active TSS	HSMMtube	muscle
27	chr8:52809800-52813200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr8:52809800-52813200	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr8:52809800-52813200	Active TSS	Colonic Mucosa	Colon
30	chr8:52809800-52813400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr8:52809800-52813400	Active TSS	Psoas Muscle	Psoas
32	chr8:52809800-52813800	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr8:52810000-52813000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr8:52810000-52813000	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr8:52810000-52813000	Active TSS	Brain Angular Gyrus	brain
36	chr8:52810000-52813000	Active TSS	Fetal Intestine Small	intestine
37	chr8:52810000-52813000	Active TSS	NHEK	skin
38	chr8:52810000-52813200	Active TSS	H9 Cell Line	embryonic stem cell
39	chr8:52810200-52813000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr8:52810200-52813000	Active TSS	Left Ventricle	heart
41	chr8:52810200-52813000	Active TSS	Rectal Smooth Muscle	rectum
42	chr8:52810200-52813200	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr8:52810200-52813400	Active TSS	Fetal Muscle Trunk	muscle
44	chr8:52810200-52813800	Active TSS	Pancreas	Pancrea
45	chr8:52810400-52813400	Active TSS	Lung	lung
46	chr8:52810600-52813000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr8:52810600-52813000	Active TSS	Small Intestine	intestine
48	chr8:52811800-52813000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr8:52811800-52813200	Active TSS	Fetal Brain Male	brain
50	chr8:52812000-52813200	Active TSS	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links