Variant report

Variant	rs12365962
Chromosome Location	chr11:35161288-35161289
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	chr11:35160353-35161377	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:35160236-35161886	GM18951	blood:	n/a	n/a
4	RAD21	chr11:35160991-35161753	SK-N-SH_RA	brain:	n/a	n/a
5	POLR2A	chr11:35160323-35162347	GM12878	blood:	n/a	n/a
6	MAX	chr11:35160429-35161515	MCF-7	breast:	n/a	chr11:35161193-35161203 chr11:35160823-35160833
7	ZBTB7A	chr11:35160237-35161477	ECC-1	luminal epithelium:	n/a	n/a
8	ELK1	chr11:35161226-35161625	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr11:35160986-35161406	ECC-1	luminal epithelium:	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	MAX	chr11:35160391-35161362	GM12878	blood:	n/a	chr11:35161193-35161203 chr11:35160823-35160833
13	POLR2A	chr11:35160288-35162443	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:35159893-35163743	Hela-S3	cervix:	n/a	n/a
15	MXI1	chr11:35159789-35167151	IMR90	lung:	n/a	n/a
16	CTCF	chr11:35161280-35161430	SAEC	small airway:	n/a	n/a
17	MAX	chr11:35159898-35161398	SK-N-SH	brain:	n/a	chr11:35161193-35161203 chr11:35160823-35160833
18	RAD21	chr11:35161005-35161807	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr11:35161180-35161330	HAc	cerebellar:	n/a	n/a
20	MYC	chr11:35160524-35161597	MCF10A-Er-Src	breast:	n/a	chr11:35161193-35161203 chr11:35160823-35160833
21	YY1	chr11:35160915-35161383	ECC-1	luminal epithelium:	n/a	chr11:35160943-35160955 chr11:35160979-35160993
22	POLR2A	chr11:35160308-35162535	GM12891	blood:	n/a	n/a
23	MTA3	chr11:35159898-35161905	GM12878	blood:	n/a	n/a
24	EBF1	chr11:35160001-35161428	GM12878	blood:	n/a	n/a
25	POLR2A	chr11:35160396-35161508	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr11:35160385-35161980	GM12878	blood:	n/a	n/a
27	POLR2A	chr11:35161128-35161371	A549	lung:	n/a	n/a
28	RAD21	chr11:35160876-35161326	A549	lung:	n/a	n/a
29	BCLAF1	chr11:35160437-35161511	GM12878	blood:	n/a	chr11:35160547-35160556
30	POLR2A	chr11:35158320-35197578	PANC-1	pancreas:	n/a	n/a
31	REST	chr11:35160379-35161368	PANC-1	pancreas:	n/a	chr11:35160811-35160819 chr11:35160401-35160414 chr11:35160931-35160944 chr11:35160569-35160582
32	POLR2A	chr11:35160056-35161804	GM19193	blood:	n/a	n/a
33	POLR2A	chr11:35160199-35161775	Hela-S3	cervix:	n/a	n/a
34	MAX	chr11:35160451-35161484	MCF-7	breast:	n/a	chr11:35161193-35161203 chr11:35160823-35160833
35	E2F6	chr11:35159850-35161398	H1-hESC	embryonic stem cell:	n/a	chr11:35160329-35160336 chr11:35160974-35160984 chr11:35160404-35160414 chr11:35160329-35160336 chr11:35160329-35160336
36	POLR2A	chr11:35160005-35162115	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr11:35161092-35161368	H1-hESC	embryonic stem cell:	n/a	n/a
38	CHD2	chr11:35160523-35161624	GM12878	blood:	n/a	n/a
39	POLR2A	chr11:35160212-35162092	GM12892	blood:	n/a	n/a
40	POLR2A	chr11:35159386-35163856	PANC-1	pancreas:	n/a	n/a
41	CTBP2	chr11:35160070-35161420	H1-hESC	embryonic stem cell:	n/a	n/a
42	HDAC2	chr11:35160643-35161360	MCF-7	breast:	n/a	chr11:35161117-35161131 chr11:35161123-35161137 chr11:35161126-35161140 chr11:35161118-35161132
43	CEBPB	chr11:35161257-35161320	H1-hESC	embryonic stem cell:	n/a	n/a
44	MYC	chr11:35159955-35161904	NB4	blood:	n/a	chr11:35161193-35161203 chr11:35160823-35160833 chr11:35161717-35161726
45	TCF12	chr11:35160160-35161326	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr11:35160233-35161993	HL-60	blood:	n/a	n/a
47	POLR2A	chr11:35160249-35162402	GM12892	blood:	n/a	n/a
48	POLR2A	chr11:35160304-35162246	GM19099	blood:	n/a	n/a
49	TAF1	chr11:35160427-35161740	ECC-1	luminal epithelium:	n/a	n/a
50	CHD1	chr11:35159647-35163874	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:35160506..35161348-chr5:172198026..172198579,2	Hela-S3	cervix:
2	chr1:207503349..207504173-chr11:35160887..35161695,2	Hela-S3	cervix:
3	chr11:35160324..35161311-chr3:14444116..14444878,2	Hela-S3	cervix:
4	chr11:35160584..35161366-chr17:72983348..72984211,2	Hela-S3	cervix:
5	chr11:35160872..35161372-chr12:14923610..14924453,2	Hela-S3	cervix:
6	chr11:35059235..35060888-chr11:35161011..35163300,2	MCF-7	breast:
7	chr11:35160960..35162794-chr11:35186248..35188654,2	MCF-7	breast:
8	chr1:154154871..154155752-chr11:35160501..35161403,2	Hela-S3	cervix:
9	chr1:153930650..153931150-chr11:35161047..35161739,2	Hela-S3	cervix:
10	chr1:89149746..89150285-chr11:35160701..35161440,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000255521	TF binding region
ENSG00000120129	Chromatin interaction
ENSG00000065243	Chromatin interaction
ENSG00000160741	Chromatin interaction
ENSG00000197837	Chromatin interaction
ENSG00000109089	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000131389	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[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]
rs12362973	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	chr11:35160000-35161400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr11:35160000-35161600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
6	chr11:35160000-35161800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
7	chr11:35160000-35161800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
8	chr11:35160000-35162000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr11:35160000-35163400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:35160000-35163600	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr11:35160200-35161400	Active TSS	Gastric	stomach
12	chr11:35160200-35161400	Active TSS	Right Atrium	heart
13	chr11:35160200-35161600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:35160200-35161600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
15	chr11:35160200-35161600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
16	chr11:35160200-35161600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
17	chr11:35160200-35161800	Flanking Active TSS	Placenta	Placenta
18	chr11:35160200-35162000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:35160200-35162000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr11:35160200-35162200	Active TSS	Colon Smooth Muscle	Colon
21	chr11:35160200-35162800	Active TSS	A549	lung
22	chr11:35160200-35163000	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr11:35160200-35163600	Active TSS	Brain Substantia Nigra	brain
24	chr11:35160200-35165000	Active TSS	Rectal Smooth Muscle	rectum
25	chr11:35160200-35170200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
26	chr11:35160400-35161400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr11:35160400-35161400	Active TSS	Esophagus	oesophagus
28	chr11:35160400-35161400	Active TSS	Fetal Lung	lung
29	chr11:35160400-35161400	Bivalent/Poised TSS	Fetal Stomach	stomach
30	chr11:35160400-35161400	Active TSS	Lung	lung
31	chr11:35160400-35161400	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr11:35160400-35161400	Active TSS	HUVEC	blood vessel
33	chr11:35160400-35161400	Active TSS	NH-A	brain
34	chr11:35160400-35161600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
35	chr11:35160400-35161600	Active TSS	Ovary	ovary
36	chr11:35160400-35161600	Active TSS	Stomach Smooth Muscle	stomach
37	chr11:35160400-35161600	Active TSS	Hela-S3	cervix
38	chr11:35160400-35161800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
39	chr11:35160400-35161800	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr11:35160400-35161800	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr11:35160400-35162000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr11:35160400-35162000	Active TSS	Psoas Muscle	Psoas
43	chr11:35160400-35162200	Active TSS	NHDF-Ad	bronchial
44	chr11:35160400-35162600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr11:35160400-35162600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr11:35160400-35162600	Active TSS	Primary T cells from cord blood	blood
47	chr11:35160400-35162600	Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr11:35160400-35162600	Active TSS	Osteobl	bone
49	chr11:35160400-35162800	Active TSS	HSMM	muscle
50	chr11:35160400-35163000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links