Variant report

Variant	rs9689522
Chromosome Location	chr6:36097740-36097741
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:36097665-36098499	MCF10A-Er-Src	breast:	n/a	n/a
2	NFIC	chr6:36097646-36097980	GM12878	blood:	n/a	n/a
3	RUNX3	chr6:36097513-36097914	GM12878	blood:	n/a	n/a
4	MAFK	chr6:36097739-36097914	IMR90	lung:	n/a	n/a
5	POLR2A	chr6:36097730-36099330	HCT-116	colon:	n/a	n/a
6	MYC	chr6:36097597-36097792	MCF10A-Er-Src	breast:	n/a	n/a
7	HEY1	chr6:36097516-36099900	HepG2	liver:	n/a	chr6:36098036-36098051
8	MYBL2	chr6:36097735-36098235	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:36097614-36099831	HCT-116	colon:	n/a	n/a
10	RUNX3	chr6:36097567-36097859	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:36097605-36098447	MCF10A-Er-Src	breast:	n/a	n/a
12	EBF1	chr6:36097636-36097949	GM12878	blood:	n/a	chr6:36097821-36097832
13	EBF1	chr6:36097662-36098008	GM12878	blood:	n/a	chr6:36097821-36097832

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:36097692-36097742	HCM	heart:	n/a
2	chr6:36097692-36097742	NHBE	bronchial:	n/a
3	chr6:36097692-36097742	HRE	kidney:	n/a
4	chr6:36097692-36097742	HRPEpiC	eye:	n/a
5	chr6:36097692-36097742	GM12891	blood:	n/a
6	chr6:36097692-36097742	HNPCEpiC	eye:	n/a
7	chr6:36097692-36097742	NB4	blood:	n/a
8	chr6:36097692-36097742	AG04450	lung:	fetal
9	chr6:36097692-36097742	Hepatocyte	liver:	n/a
10	chr6:36097692-36097742	HCF	heart:	n/a
11	chr6:36097692-36097742	MCF10A-Er-Src	breast:	n/a
12	chr6:36097692-36097742	IMR90	lung:	fetal
13	chr6:36097692-36097742	HPAEpiC	pulmonary alveolar:	n/a
14	chr6:36097692-36097742	HEK293	kidney:	embryo
15	chr6:36097692-36097742	NT2-D1	testis:	n/a
16	chr6:36097692-36097742	Jurkat	blood:	n/a
17	chr6:36097692-36097742	AoSMC	blood vessel:	n/a
18	chr6:36097692-36097742	PANC-1	pancreas:	n/a
19	chr6:36097692-36097742	AG10803	skin:	n/a
20	chr6:36097692-36097742	BE2_C	brain:	n/a
21	chr6:36097692-36097742	AG09319	gingival:	n/a
22	chr6:36097692-36097742	HEEpiC	esophagus:	n/a
23	chr6:36097692-36097742	H1-hESC	embryonic stem cell:	embryo
24	chr6:36097692-36097742	HAEpiC	amniotic membrane:	n/a
25	chr6:36097692-36097742	ProgFib	skin:	n/a
26	chr6:36097692-36097742	NHDF-neo	bronchial:	n/a
27	chr6:36097692-36097742	HepG2	liver:	n/a
28	chr6:36097692-36097742	A549	lung:	n/a
29	chr6:36097692-36097742	AG09309	skin:	n/a
30	chr6:36097692-36097742	HCPEpiC	choroid plexus:	n/a
31	chr6:36097692-36097742	PrEC	prostate:	n/a
32	chr6:36097692-36097742	GM06990	blood:	n/a
33	chr6:36097692-36097742	MCF-7	breast:	n/a
34	chr6:36097692-36097742	GM19239	blood:	n/a
35	chr6:36097692-36097742	BJ	skin:	n/a
36	chr6:36097692-36097742	HRCEpiC	kidney:	n/a
37	chr6:36097692-36097742	SK-N-SH	brain:	n/a
38	chr6:36097692-36097742	AG04449	skin:	fetal
39	chr6:36097692-36097742	T-47D	breast:	n/a
40	chr6:36097692-36097742	SKMC	muscle:	n/a
41	chr6:36097692-36097742	SK-N-SH_RA	brain:	n/a
42	chr6:36097692-36097742	HUVEC	blood vessel:	n/a
43	chr6:36097692-36097742	GM12878	blood:	n/a
44	chr6:36097692-36097742	ovcar-3	ovarian:	n/a
45	chr6:36097692-36097742	LNCaP	prostate:	n/a
46	chr6:36097692-36097742	NH-A	brain:	n/a
47	chr6:36097692-36097742	K562	blood:	n/a
48	chr6:36097692-36097742	PFSK-1	brain:	n/a
49	chr6:36097692-36097742	CMK	blood:	n/a
50	chr6:36097692-36097742	HCT-116	colon:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr6:36097672..36103046-chr6:36163327..36166048,5	MCF-7	breast:
2	chr6:36097129..36099054-chr6:36162391..36164603,2	K562	blood:
3	chr6:36096617..36099142-chr6:36162886..36164936,2	MCF-7	breast:

No data

Variant related genes	Relation type
MAPK13	TF binding region
MAPK13	CpG island
ENSG00000096070	Chromatin interaction
ENSG00000246982	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11759995	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs763096	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9689951	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9689522	RNF8	cis	cerebellum	SCAN
rs9689522	PI16	cis	cerebellum	SCAN
rs9689522	MDGA1	cis	parietal	SCAN
rs9689522	SNRPC	cis	cerebellum	SCAN
rs9689522	C6orf125	cis	parietal	SCAN
rs9689522	MAPK14	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36086600-36098000	Weak transcription	Aorta	Aorta
2	chr6:36089000-36097800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:36089400-36097800	Enhancers	Primary T cells fromperipheralblood	blood
4	chr6:36089600-36097800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:36091800-36097800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:36091800-36097800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:36091800-36097800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:36091800-36097800	Weak transcription	Right Atrium	heart
9	chr6:36091800-36098000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:36092200-36097800	Weak transcription	Liver	Liver
11	chr6:36093800-36097800	Enhancers	NHDF-Ad	bronchial
12	chr6:36095000-36098000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:36095400-36097800	Weak transcription	Small Intestine	intestine
14	chr6:36095600-36099000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:36095800-36097800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:36095800-36097800	Weak transcription	Right Ventricle	heart
17	chr6:36095800-36097800	Weak transcription	HSMMtube	muscle
18	chr6:36096000-36097800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:36096000-36098000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:36096200-36099200	Weak transcription	HSMM	muscle
21	chr6:36096400-36099200	Weak transcription	K562	blood
22	chr6:36096600-36097800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:36096600-36099200	Weak transcription	Hela-S3	cervix
24	chr6:36096800-36097800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:36096800-36097800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:36096800-36097800	Weak transcription	Esophagus	oesophagus
27	chr6:36096800-36098000	Weak transcription	Spleen	Spleen
28	chr6:36097000-36098000	Weak transcription	Lung	lung
29	chr6:36097400-36099800	Enhancers	HUVEC	blood vessel
30	chr6:36097600-36097800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
31	chr6:36097600-36097800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
32	chr6:36097600-36097800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:36097600-36097800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:36097600-36097800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:36097600-36097800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:36097600-36097800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
37	chr6:36097600-36097800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
38	chr6:36097600-36097800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:36097600-36097800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr6:36097600-36097800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr6:36097600-36097800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:36097600-36097800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:36097600-36097800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr6:36097600-36097800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:36097600-36097800	Flanking Active TSS	Brain Angular Gyrus	brain
46	chr6:36097600-36097800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
47	chr6:36097600-36097800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:36097600-36097800	Active TSS	Colonic Mucosa	Colon
49	chr6:36097600-36097800	Bivalent Enhancer	Colon Smooth Muscle	Colon
50	chr6:36097600-36097800	Enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links