Variant report

Variant	rs2430978
Chromosome Location	chr11:65816656-65816657
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:183)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65816137-65816708	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr11:65816276-65816784	H1-hESC	embryonic stem cell:	n/a	chr11:65816358-65816368
3	POLR2A	chr11:65816394-65816683	H1-hESC	embryonic stem cell:	n/a	n/a
4	TAF1	chr11:65816423-65816679	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr11:65816357-65816904	H1-hESC	embryonic stem cell:	n/a	chr11:65816358-65816368
6	POLR2A	chr11:65816368-65816767	SK-N-SH	brain:	n/a	n/a
7	TAF1	chr11:65816254-65816668	H1-hESC	embryonic stem cell:	n/a	n/a
8	TBP	chr11:65816456-65816667	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr11:65816358-65816771	H1-neurons	neurons:	n/a	n/a
10	REST	chr11:65816058-65816947	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr11:65816370-65816822	H1-neurons	neurons:	n/a	n/a
12	MXI1	chr11:65816095-65817543	SK-N-SH	brain:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:65816642-65816692	SK-N-SH_RA	brain:	n/a
2	chr11:65816642-65816692	HL-60	blood:	n/a
3	chr11:65816655-65816705	HRCEpiC	kidney:	n/a
4	chr11:65816646-65816696	NB4	blood:	n/a
5	chr11:65816642-65816692	MCF-7	breast:	n/a
6	chr11:65816642-65816692	HCT-116	colon:	n/a
7	chr11:65816642-65816692	T-47D	breast:	n/a
8	chr11:65816642-65816692	SKMC	muscle:	n/a
9	chr11:65816646-65816696	HEK293	kidney:	embryo
10	chr11:65816655-65816705	K562	blood:	n/a
11	chr11:65816646-65816696	HIPEpiC	eye:	n/a
12	chr11:65816646-65816696	HCT-116	colon:	n/a
13	chr11:65816655-65816705	HRPEpiC	eye:	n/a
14	chr11:65816655-65816705	HCF	heart:	n/a
15	chr11:65816655-65816705	HUVEC	blood vessel:	n/a
16	chr11:65816642-65816692	HCF	heart:	n/a
17	chr11:65816646-65816696	HRCEpiC	kidney:	n/a
18	chr11:65816646-65816696	HCF	heart:	n/a
19	chr11:65816655-65816705	HL-60	blood:	n/a
20	chr11:65816646-65816696	K562	blood:	n/a
21	chr11:65816642-65816692	HPAEpiC	pulmonary alveolar:	n/a
22	chr11:65816642-65816692	RPTEC	kidney:	n/a
23	chr11:65816646-65816696	Hela-S3	cervix:	n/a
24	chr11:65816646-65816696	GM19239	blood:	n/a
25	chr11:65816646-65816696	MCF10A-Er-Src	breast:	n/a
26	chr11:65816655-65816705	AG09319	gingival:	n/a
27	chr11:65816646-65816696	HCPEpiC	choroid plexus:	n/a
28	chr11:65816655-65816705	PANC-1	pancreas:	n/a
29	chr11:65816642-65816692	K562	blood:	n/a
30	chr11:65816646-65816696	SKMC	muscle:	n/a
31	chr11:65816646-65816696	SK-N-SH_RA	brain:	n/a
32	chr11:65816655-65816705	HCM	heart:	n/a
33	chr11:65816646-65816696	NHDF-neo	bronchial:	n/a
34	chr11:65816642-65816692	ovcar-3	ovarian:	n/a
35	chr11:65816655-65816705	LNCaP	prostate:	n/a
36	chr11:65816646-65816696	GM12892	blood:	n/a
37	chr11:65816646-65816696	HPAEpiC	pulmonary alveolar:	n/a
38	chr11:65816642-65816692	HUVEC	blood vessel:	n/a
39	chr11:65816646-65816696	AoSMC	blood vessel:	n/a
40	chr11:65816655-65816705	MCF10A-Er-Src	breast:	n/a
41	chr11:65816642-65816692	PrEC	prostate:	n/a
42	chr11:65816646-65816696	ovcar-3	ovarian:	n/a
43	chr11:65816646-65816696	AG09309	skin:	n/a
44	chr11:65816646-65816696	RPTEC	kidney:	n/a
45	chr11:65816655-65816705	NT2-D1	testis:	n/a
46	chr11:65816655-65816705	U87	brain:	n/a
47	chr11:65816646-65816696	NT2-D1	testis:	n/a
48	chr11:65816642-65816692	IMR90	lung:	fetal
49	chr11:65816655-65816705	HRE	kidney:	n/a
50	chr11:65816642-65816692	Jurkat	blood:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65815755..65817643-chr11:65824543..65827517,2	MCF-7	breast:
2	chr11:65768713..65771187-chr11:65815106..65817250,2	MCF-7	breast:
3	chr11:65792176..65796965-chr11:65812595..65817477,5	MCF-7	breast:
4	chr11:65815354..65817680-chr11:65821630..65823726,2	K562	blood:
5	chr11:65811021..65815121-chr11:65816503..65821449,7	K562	blood:

No data

Variant related genes	Relation type
SF3B2	TF binding region
ENSG00000238752	TF binding region
GAL3ST3	TF binding region
ENSG00000238752	CpG island
GAL3ST3	CpG island
SF3B2	CpG island
ENSG00000175376	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000175294	Chromatin interaction
ENSG00000175229	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11227384	0.95[ASN][1000 genomes]
rs1642958	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1783563	0.90[ASN][1000 genomes]
rs2241303	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576	0.96[ASN][1000 genomes]
rs2845570	0.81[ASN][1000 genomes]
rs4930170	0.95[ASN][1000 genomes]
rs493320	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs539046	0.84[AMR][1000 genomes]
rs570760	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs571374	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs574335	0.94[EUR][1000 genomes]
rs576836	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs577013	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72932627	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription 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	61 gene(s)	inside rSNPs	diseases
3	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv897770	chr11:65803750-65824472	Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65790400-65818600	Weak transcription	HSMM	muscle
2	chr11:65813000-65818200	Weak transcription	Lung	lung
3	chr11:65813200-65817200	Weak transcription	Hela-S3	cervix
4	chr11:65813200-65818200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:65813200-65818200	Weak transcription	Spleen	Spleen
6	chr11:65813200-65818400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:65813200-65818800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr11:65813400-65816800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr11:65813400-65817600	Weak transcription	K562	blood
10	chr11:65813400-65818200	Weak transcription	A549	lung
11	chr11:65813600-65818200	Weak transcription	Dnd41	blood
12	chr11:65814200-65819200	Enhancers	Pancreas	Pancrea
13	chr11:65814400-65818800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr11:65815000-65817200	Enhancers	Fetal Brain Male	brain
15	chr11:65815000-65817200	Enhancers	Fetal Heart	heart
16	chr11:65815400-65817000	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr11:65815400-65817200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr11:65815600-65816800	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr11:65815600-65816800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:65815800-65816800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr11:65815800-65816800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
22	chr11:65815800-65816800	Active TSS	Right Atrium	heart
23	chr11:65815800-65817000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:65815800-65817000	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr11:65815800-65818200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr11:65815800-65818400	Weak transcription	Fetal Kidney	kidney
27	chr11:65816000-65816800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:65816000-65816800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:65816000-65816800	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr11:65816000-65816800	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr11:65816000-65816800	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr11:65816000-65816800	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr11:65816000-65816800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr11:65816000-65817000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:65816000-65817000	Active TSS	Brain Angular Gyrus	brain
36	chr11:65816000-65817000	Active TSS	Brain Anterior Caudate	brain
37	chr11:65816000-65817000	Active TSS	Fetal Brain Female	brain
38	chr11:65816200-65816800	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr11:65816200-65816800	Active TSS	H1 Cell Line	embryonic stem cell
40	chr11:65816200-65816800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr11:65816200-65817200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr11:65816200-65817200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr11:65816200-65817200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:65816200-65817200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
45	chr11:65816200-65817400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
46	chr11:65816400-65816800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:65816400-65816800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr11:65816400-65817000	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr11:65816400-65817000	Active TSS	Brain Germinal Matrix	brain
50	chr11:65816400-65817000	Flanking Active TSS	Thymus	Thymus

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