Variant report

Variant	rs12362973
Chromosome Location	chr11:35161423-35161424
allele	A/G
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	E2F6	chr11:35159983-35161664	Hela-S3	cervix:	n/a	chr11:35160329-35160336 chr11:35160974-35160984 chr11:35160404-35160414 chr11:35160329-35160336 chr11:35160329-35160336
2	POLR2A	chr11:35160236-35161886	GM18951	blood:	n/a	n/a
3	RAD21	chr11:35160991-35161753	SK-N-SH_RA	brain:	n/a	n/a
4	POLR2A	chr11:35160323-35162347	GM12878	blood:	n/a	n/a
5	MAX	chr11:35160429-35161515	MCF-7	breast:	n/a	chr11:35161193-35161203 chr11:35160823-35160833
6	POLR2A	chr11:35161383-35161777	GM12878	blood:	n/a	n/a
7	ZBTB7A	chr11:35160237-35161477	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr11:35161388-35161977	GM12891	blood:	n/a	n/a
9	ELK1	chr11:35161226-35161625	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr11:35160258-35161769	Hela-S3	cervix:	n/a	n/a
11	WRNIP1	chr11:35160974-35161928	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:35160288-35162443	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:35159893-35163743	Hela-S3	cervix:	n/a	n/a
14	MXI1	chr11:35159789-35167151	IMR90	lung:	n/a	n/a
15	CTCF	chr11:35161280-35161430	SAEC	small airway:	n/a	n/a
16	RAD21	chr11:35161005-35161807	Hela-S3	cervix:	n/a	n/a
17	MYC	chr11:35160524-35161597	MCF10A-Er-Src	breast:	n/a	chr11:35161193-35161203 chr11:35160823-35160833
18	POLR2A	chr11:35160308-35162535	GM12891	blood:	n/a	n/a
19	MTA3	chr11:35159898-35161905	GM12878	blood:	n/a	n/a
20	EBF1	chr11:35160001-35161428	GM12878	blood:	n/a	n/a
21	POLR2A	chr11:35160396-35161508	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr11:35160385-35161980	GM12878	blood:	n/a	n/a
23	BCLAF1	chr11:35160437-35161511	GM12878	blood:	n/a	chr11:35160547-35160556
24	POLR2A	chr11:35158320-35197578	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr11:35160056-35161804	GM19193	blood:	n/a	n/a
26	POLR2A	chr11:35160199-35161775	Hela-S3	cervix:	n/a	n/a
27	MAX	chr11:35160451-35161484	MCF-7	breast:	n/a	chr11:35161193-35161203 chr11:35160823-35160833
28	POLR2A	chr11:35160005-35162115	Hela-S3	cervix:	n/a	n/a
29	CHD2	chr11:35160523-35161624	GM12878	blood:	n/a	n/a
30	POLR2A	chr11:35160212-35162092	GM12892	blood:	n/a	n/a
31	POLR2A	chr11:35159386-35163856	PANC-1	pancreas:	n/a	n/a
32	MYC	chr11:35159955-35161904	NB4	blood:	n/a	chr11:35161193-35161203 chr11:35160823-35160833 chr11:35161717-35161726
33	POLR2A	chr11:35160233-35161993	HL-60	blood:	n/a	n/a
34	POLR2A	chr11:35160249-35162402	GM12892	blood:	n/a	n/a
35	POLR2A	chr11:35160304-35162246	GM19099	blood:	n/a	n/a
36	TAF1	chr11:35160427-35161740	ECC-1	luminal epithelium:	n/a	n/a
37	CHD1	chr11:35159647-35163874	IMR90	lung:	n/a	n/a
38	POLR2A	chr11:35160313-35161779	GM12878	blood:	n/a	n/a
39	MAX	chr11:35160121-35161423	H1-hESC	embryonic stem cell:	n/a	chr11:35161193-35161203 chr11:35160823-35160833
40	MAX	chr11:35159859-35161442	ECC-1	luminal epithelium:	n/a	chr11:35161193-35161203 chr11:35160823-35160833
41	POLR2A	chr11:35159892-35169475	U87	brain:	n/a	n/a
42	TAF1	chr11:35160467-35161439	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr11:35160212-35162140	GM12878	blood:	n/a	n/a
44	ELF1	chr11:35160216-35161548	GM12878	blood:	n/a	chr11:35160779-35160791
45	SMC3	chr11:35159921-35162245	Hela-S3	cervix:	n/a	chr11:35160781-35160791
46	POLR2A	chr11:35159882-35169364	GM12891	blood:	n/a	n/a
47	POLR2A	chr11:35161167-35161441	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr11:35160384-35161808	NB4	blood:	n/a	n/a
49	POLR2A	chr11:35160187-35161424	HCT-116	colon:	n/a	n/a
50	POLR2A	chr11:35160060-35161829	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:207503349..207504173-chr11:35160887..35161695,2	Hela-S3	cervix:
2	chr11:35059235..35060888-chr11:35161011..35163300,2	MCF-7	breast:
3	chr11:35160960..35162794-chr11:35186248..35188654,2	MCF-7	breast:
4	chr1:153930650..153931150-chr11:35161047..35161739,2	Hela-S3	cervix:
5	chr1:89149746..89150285-chr11:35160701..35161440,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000255521	TF binding region
ENSG00000065243	Chromatin interaction
ENSG00000160741	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11033004	1.00[ASN][1000 genomes]
rs11033008	1.00[CEU][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362140	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12365962	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756192	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv540999	chr11:35021936-35185471	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	esv2758263	chr11:35029933-35226784	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv2759818	chr11:35029933-35238578	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv541000	chr11:35053717-35185471	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv541001	chr11:35053717-35224624	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv2757437	chr11:35067482-35238578	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	esv2752912	chr11:35074167-35238578	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv508623	chr11:35094933-35203363	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv541002	chr11:35101282-35224624	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv541003	chr11:35122694-35261451	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
12	nsv541004	chr11:35122694-35297414	Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35159800-35163600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr11:35159800-35163600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr11:35159800-35165000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:35160000-35161600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
5	chr11:35160000-35161800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
6	chr11:35160000-35161800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
7	chr11:35160000-35162000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr11:35160000-35163400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:35160000-35163600	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr11:35160200-35161600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:35160200-35161600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
12	chr11:35160200-35161600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
13	chr11:35160200-35161600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
14	chr11:35160200-35161800	Flanking Active TSS	Placenta	Placenta
15	chr11:35160200-35162000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:35160200-35162000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr11:35160200-35162200	Active TSS	Colon Smooth Muscle	Colon
18	chr11:35160200-35162800	Active TSS	A549	lung
19	chr11:35160200-35163000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr11:35160200-35163600	Active TSS	Brain Substantia Nigra	brain
21	chr11:35160200-35165000	Active TSS	Rectal Smooth Muscle	rectum
22	chr11:35160200-35170200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
23	chr11:35160400-35161600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
24	chr11:35160400-35161600	Active TSS	Ovary	ovary
25	chr11:35160400-35161600	Active TSS	Stomach Smooth Muscle	stomach
26	chr11:35160400-35161600	Active TSS	Hela-S3	cervix
27	chr11:35160400-35161800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr11:35160400-35161800	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr11:35160400-35161800	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr11:35160400-35162000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr11:35160400-35162000	Active TSS	Psoas Muscle	Psoas
32	chr11:35160400-35162200	Active TSS	NHDF-Ad	bronchial
33	chr11:35160400-35162600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:35160400-35162600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:35160400-35162600	Active TSS	Primary T cells from cord blood	blood
36	chr11:35160400-35162600	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr11:35160400-35162600	Active TSS	Osteobl	bone
38	chr11:35160400-35162800	Active TSS	HSMM	muscle
39	chr11:35160400-35163000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr11:35160400-35163000	Active TSS	Aorta	Aorta
41	chr11:35160400-35163200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:35160400-35163200	Active TSS	Pancreas	Pancrea
43	chr11:35160400-35163200	Active TSS	Small Intestine	intestine
44	chr11:35160400-35163400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr11:35160400-35163400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:35160400-35163400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr11:35160400-35164000	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr11:35160400-35164000	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr11:35160600-35161600	Active TSS	Muscle Satellite Cultured Cells	--
50	chr11:35160600-35161600	Flanking Active TSS	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links