Variant report

Variant	rs353558
Chromosome Location	chr11:35161670-35161671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:83)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:83 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:35160236-35161886	GM18951	blood:	n/a	n/a
2	RAD21	chr11:35160991-35161753	SK-N-SH_RA	brain:	n/a	n/a
3	POLR2A	chr11:35160323-35162347	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:35161383-35161777	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:35161388-35161977	GM12891	blood:	n/a	n/a
6	POLR2A	chr11:35160258-35161769	Hela-S3	cervix:	n/a	n/a
7	WRNIP1	chr11:35160974-35161928	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:35160288-35162443	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:35159893-35163743	Hela-S3	cervix:	n/a	n/a
10	MXI1	chr11:35159789-35167151	IMR90	lung:	n/a	n/a
11	RAD21	chr11:35161005-35161807	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr11:35160308-35162535	GM12891	blood:	n/a	n/a
13	MTA3	chr11:35159898-35161905	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:35160385-35161980	GM12878	blood:	n/a	n/a
15	SMC3	chr11:35161647-35161810	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:35158320-35197578	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr11:35160056-35161804	GM19193	blood:	n/a	n/a
18	POLR2A	chr11:35160199-35161775	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr11:35160005-35162115	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr11:35160212-35162092	GM12892	blood:	n/a	n/a
21	POLR2A	chr11:35159386-35163856	PANC-1	pancreas:	n/a	n/a
22	MYC	chr11:35159955-35161904	NB4	blood:	n/a	chr11:35161193-35161203 chr11:35160823-35160833 chr11:35161717-35161726
23	POLR2A	chr11:35160233-35161993	HL-60	blood:	n/a	n/a
24	POLR2A	chr11:35160249-35162402	GM12892	blood:	n/a	n/a
25	POLR2A	chr11:35160304-35162246	GM19099	blood:	n/a	n/a
26	TAF1	chr11:35160427-35161740	ECC-1	luminal epithelium:	n/a	n/a
27	CHD1	chr11:35159647-35163874	IMR90	lung:	n/a	n/a
28	POLR2A	chr11:35161528-35161932	HCT-116	colon:	n/a	n/a
29	POLR2A	chr11:35160313-35161779	GM12878	blood:	n/a	n/a
30	POLR2A	chr11:35159892-35169475	U87	brain:	n/a	n/a
31	POLR2A	chr11:35160212-35162140	GM12878	blood:	n/a	n/a
32	SMC3	chr11:35159921-35162245	Hela-S3	cervix:	n/a	chr11:35160781-35160791
33	POLR2A	chr11:35159882-35169364	GM12891	blood:	n/a	n/a
34	POLR2A	chr11:35160384-35161808	NB4	blood:	n/a	n/a
35	POLR2A	chr11:35160060-35161829	HCT-116	colon:	n/a	n/a
36	POLR2A	chr11:35160230-35163769	IMR90	lung:	n/a	n/a
37	POLR2A	chr11:35159651-35162279	GM18505	blood:	n/a	n/a
38	POLR2A	chr11:35159950-35178999	U87	brain:	n/a	n/a
39	RAD21	chr11:35160186-35162198	IMR90	lung:	n/a	n/a
40	MAX	chr11:35159963-35161716	Hela-S3	cervix:	n/a	chr11:35161193-35161203 chr11:35160823-35160833
41	RFX5	chr11:35160059-35161866	Hela-S3	cervix:	n/a	n/a
42	TBP	chr11:35160091-35162015	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr11:35160281-35161916	GM15510	blood:	n/a	n/a
44	CEBPB	chr11:35161156-35161815	Hela-S3	cervix:	n/a	n/a
45	TAF1	chr11:35160079-35161804	Hela-S3	cervix:	n/a	n/a
46	TCF7L2	chr11:35160176-35161860	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr11:35160199-35163808	U87	brain:	n/a	n/a
48	EBF1	chr11:35161491-35161680	GM12878	blood:	n/a	n/a
49	SMARCC1	chr11:35159921-35161715	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr11:35159686-35169512	GM12892	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

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:

No data

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

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2553808	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2553809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2732571	0.83[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs353625	0.80[CHB][hapmap];0.82[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs353558	CCDC73	cis	cerebellum	SCAN

Chromatin state (count:117 , 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	chr11:35160000-35161800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr11:35160000-35161800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
6	chr11:35160000-35162000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr11:35160000-35163400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:35160000-35163600	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr11:35160200-35161800	Flanking Active TSS	Placenta	Placenta
10	chr11:35160200-35162000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:35160200-35162000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr11:35160200-35162200	Active TSS	Colon Smooth Muscle	Colon
13	chr11:35160200-35162800	Active TSS	A549	lung
14	chr11:35160200-35163000	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr11:35160200-35163600	Active TSS	Brain Substantia Nigra	brain
16	chr11:35160200-35165000	Active TSS	Rectal Smooth Muscle	rectum
17	chr11:35160200-35170200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
18	chr11:35160400-35161800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr11:35160400-35161800	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr11:35160400-35161800	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr11:35160400-35162000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr11:35160400-35162000	Active TSS	Psoas Muscle	Psoas
23	chr11:35160400-35162200	Active TSS	NHDF-Ad	bronchial
24	chr11:35160400-35162600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:35160400-35162600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:35160400-35162600	Active TSS	Primary T cells from cord blood	blood
27	chr11:35160400-35162600	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr11:35160400-35162600	Active TSS	Osteobl	bone
29	chr11:35160400-35162800	Active TSS	HSMM	muscle
30	chr11:35160400-35163000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:35160400-35163000	Active TSS	Aorta	Aorta
32	chr11:35160400-35163200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:35160400-35163200	Active TSS	Pancreas	Pancrea
34	chr11:35160400-35163200	Active TSS	Small Intestine	intestine
35	chr11:35160400-35163400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr11:35160400-35163400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:35160400-35163400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:35160400-35164000	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr11:35160400-35164000	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr11:35160600-35161800	Active TSS	Primary B cells from peripheral blood	blood
41	chr11:35160600-35161800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:35160600-35162000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr11:35160600-35162400	Active TSS	Primary monocytes fromperipheralblood	blood
44	chr11:35160600-35162400	Active TSS	Primary T cells fromperipheralblood	blood
45	chr11:35160600-35162400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
46	chr11:35160600-35162400	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr11:35160600-35162600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr11:35160600-35162600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:35160600-35162800	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr11:35160600-35164200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links