Variant report

Variant	rs10116407
Chromosome Location	chr9:16726654-16726655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:76)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:76 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr9:16726008-16728237	IMR90	lung:	n/a	chr9:16728033-16728047
2	CEBPB	chr9:16726577-16727408	A549	lung:	n/a	chr9:16726904-16726915
3	GATA3	chr9:16726607-16726680	SH-SY5Y	brain:	n/a	n/a
4	RAD21	chr9:16725585-16728531	SK-N-SH	brain:	n/a	chr9:16728033-16728047
5	POLR2A	chr9:16726653-16727107	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr9:16726587-16727480	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr9:16726630-16727554	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr9:16726611-16727437	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr9:16726496-16727626	A549	lung:	n/a	n/a
10	MYC	chr9:16726566-16727083	MCF10A-Er-Src	breast:	n/a	n/a
11	SIN3A	chr9:16726646-16728408	H1-hESC	embryonic stem cell:	n/a	n/a
12	EP300	chr9:16726226-16726983	Hela-S3	cervix:	n/a	n/a
13	E2F6	chr9:16726614-16727530	A549	lung:	n/a	n/a
14	RAD21	chr9:16726621-16727461	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr9:16726566-16727494	A549	lung:	n/a	n/a
16	BCL3	chr9:16726555-16727142	A549	lung:	n/a	n/a
17	BCL3	chr9:16726476-16727092	A549	lung:	n/a	n/a
18	POLR2A	chr9:16726496-16727599	U87	brain:	n/a	n/a
19	ZNF384	chr9:16726587-16726688	GM12878	blood:	n/a	n/a
20	SIN3AK20	chr9:16726605-16726927	A549	lung:	n/a	n/a
21	SP1	chr9:16726544-16727478	A549	lung:	n/a	n/a
22	POLR2A	chr9:16726622-16727529	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr9:16726608-16727477	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr9:16726601-16727397	SK-N-SH	brain:	n/a	n/a
25	CEBPB	chr9:16726598-16727409	ECC-1	luminal epithelium:	n/a	chr9:16726904-16726915
26	TAF1	chr9:16726617-16727449	H1-hESC	embryonic stem cell:	n/a	n/a
27	RAD21	chr9:16726639-16727396	ECC-1	luminal epithelium:	n/a	n/a
28	TAF1	chr9:16726639-16727407	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr9:16726630-16727484	NB4	blood:	n/a	n/a
30	RAD21	chr9:16726592-16727070	SK-N-SH_RA	brain:	n/a	n/a
31	TCF12	chr9:16726522-16727764	A549	lung:	n/a	n/a
32	MAX	chr9:16726642-16727721	Hela-S3	cervix:	n/a	n/a
33	GATA3	chr9:16726467-16727448	A549	lung:	n/a	chr9:16727279-16727287
34	MYC	chr9:16726640-16727717	A549	lung:	n/a	n/a
35	YY1	chr9:16726608-16727249	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr9:16726582-16727541	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr9:16726567-16727658	SK-N-MC	brain:	n/a	n/a
38	RAD21	chr9:16726609-16727461	SK-N-SH_RA	brain:	n/a	n/a
39	POLR2A	chr9:16726447-16727897	MCF10A-Er-Src	breast:	n/a	n/a
40	MAX	chr9:16726630-16727517	ECC-1	luminal epithelium:	n/a	n/a
41	CHD1	chr9:16726626-16727647	H1-hESC	embryonic stem cell:	n/a	n/a
42	ATF2	chr9:16726542-16727101	H1-hESC	embryonic stem cell:	n/a	n/a
43	GATA2	chr9:16726626-16727486	HUVEC	blood vessel:	n/a	chr9:16727279-16727287
44	POLR2A	chr9:16725793-16728460	IMR90	lung:	n/a	n/a
45	MXI1	chr9:16725393-16727631	IMR90	lung:	n/a	n/a
46	TCF7L2	chr9:16726652-16727411	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr9:16726528-16727547	HUVEC	blood vessel:	n/a	n/a
48	REST	chr9:16726468-16727241	A549	lung:	n/a	n/a
49	E2F4	chr9:16726626-16727591	MCF10A-Er-Src	breast:	n/a	n/a
50	TAF1	chr9:16726597-16727470	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:5569698..5570590-chr9:16726454..16727434,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000234779	TF binding region
ENSG00000075624	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10116469	1.00[CEU][hapmap]
rs10119731	0.91[TSI][hapmap]
rs10120562	0.81[TSI][hapmap]
rs10122736	0.86[CEU][hapmap]
rs10122827	0.85[CEU][hapmap]
rs10123118	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10738457	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10756810	0.85[EUR][1000 genomes]
rs10810595	1.00[CEU][hapmap]
rs10810599	0.89[EUR][1000 genomes]
rs10810600	0.96[EUR][1000 genomes]
rs10810602	0.85[EUR][1000 genomes]
rs10810610	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10810614	0.87[EUR][1000 genomes]
rs10810615	0.85[EUR][1000 genomes]
rs10810617	1.00[CEU][hapmap]
rs10962543	0.87[CEU][hapmap]
rs10962556	0.91[EUR][1000 genomes]
rs10962569	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10962576	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10962592	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs12238070	0.87[EUR][1000 genomes]
rs12341542	1.00[CEU][hapmap]
rs12344698	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12375507	0.87[CEU][hapmap]
rs12377846	0.85[CEU][hapmap]
rs1337386	0.96[EUR][1000 genomes]
rs1361073	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1856132	1.00[CEU][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1999214	0.91[EUR][1000 genomes]
rs2039185	1.00[CEU][hapmap]
rs2150089	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs2282072	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4961747	0.81[JPT][hapmap]
rs5016914	0.81[EUR][1000 genomes]
rs73419969	0.91[EUR][1000 genomes]
rs7855044	0.87[EUR][1000 genomes]
rs7862734	1.00[CEU][hapmap]

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	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription 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	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription 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	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv2758627	chr9:16641966-16809203	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2759673	chr9:16641966-16809203	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv892649	chr9:16677221-16761597	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16721600-16726800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:16724400-16729800	Active TSS	Ovary	ovary
3	chr9:16724800-16728800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:16725200-16729400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:16726000-16727400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr9:16726000-16727400	Active TSS	Fetal Intestine Large	intestine
7	chr9:16726000-16727800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
8	chr9:16726000-16727800	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr9:16726000-16728200	Active TSS	Colonic Mucosa	Colon
10	chr9:16726200-16726800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:16726200-16726800	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
12	chr9:16726200-16726800	Weak transcription	Lung	lung
13	chr9:16726200-16727400	Active TSS	Fetal Kidney	kidney
14	chr9:16726200-16727800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr9:16726200-16727800	Active TSS	H1 Cell Line	embryonic stem cell
16	chr9:16726200-16728000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:16726200-16728000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:16726200-16728000	Bivalent/Poised TSS	Fetal Brain Male	brain
19	chr9:16726400-16726800	Flanking Active TSS	NHEK	skin
20	chr9:16726400-16727200	Active TSS	Adipose Nuclei	Adipose
21	chr9:16726400-16727400	Active TSS	HUVEC	blood vessel
22	chr9:16726400-16727600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr9:16726400-16727600	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr9:16726400-16727800	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr9:16726400-16727800	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr9:16726400-16727800	Active TSS	Fetal Muscle Leg	muscle
27	chr9:16726400-16727800	Active TSS	A549	lung
28	chr9:16726400-16727800	Active TSS	HSMM	muscle
29	chr9:16726400-16727800	Active TSS	NH-A	brain
30	chr9:16726400-16727800	Active TSS	NHDF-Ad	bronchial
31	chr9:16726400-16727800	Active TSS	NHLF	lung
32	chr9:16726400-16727800	Active TSS	Osteobl	bone
33	chr9:16726400-16728000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:16726400-16728000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:16726400-16728000	Active TSS	Colon Smooth Muscle	Colon
36	chr9:16726400-16728000	Active TSS	Fetal Lung	lung
37	chr9:16726400-16728200	Active TSS	H9 Cell Line	embryonic stem cell
38	chr9:16726400-16728200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:16726400-16728400	Active TSS	HSMMtube	muscle
40	chr9:16726400-16729200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:16726600-16726800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr9:16726600-16726800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr9:16726600-16726800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr9:16726600-16726800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
45	chr9:16726600-16726800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:16726600-16726800	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:16726600-16726800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr9:16726600-16726800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:16726600-16726800	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr9:16726600-16726800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain

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