Variant report

Variant	rs353560
Chromosome Location	chr11:35156500-35156501
allele	A/C
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	EP300	chr11:35156105-35157361	SK-N-SH	brain:	n/a	chr11:35157134-35157148 chr11:35157316-35157325 chr11:35157317-35157326 chr11:35156260-35156274
2	EP300	chr11:35156254-35157298	SK-N-SH_RA	brain:	n/a	chr11:35157134-35157148 chr11:35156260-35156274
3	NFIC	chr11:35156403-35157331	GM12878	blood:	n/a	n/a
4	PBX3	chr11:35156167-35157360	SK-N-SH	brain:	n/a	n/a
5	EP300	chr11:35156220-35156721	SK-N-SH_RA	brain:	n/a	chr11:35156260-35156274
6	POLR2A	chr11:35156370-35157062	PANC-1	pancreas:	n/a	n/a
7	RAD21	chr11:35156278-35156587	SK-N-SH_RA	brain:	n/a	n/a
8	PBX3	chr11:35156227-35156739	SK-N-SH	brain:	n/a	n/a
9	RAD21	chr11:35156311-35156645	SK-N-SH_RA	brain:	n/a	n/a
10	GATA3	chr11:35156242-35156747	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr11:35156068-35157290	SK-N-SH	brain:	n/a	n/a
12	RUNX3	chr11:35156445-35157799	GM12878	blood:	n/a	n/a
13	GATA3	chr11:35156172-35157450	SK-N-SH	brain:	n/a	chr11:35157118-35157126
14	TCF12	chr11:35156080-35157357	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr11:35156233-35156634	SK-N-SH	brain:	n/a	n/a
16	NFIC	chr11:35156152-35157385	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:35155392..35158105-chr11:35159031..35160697,2	MCF-7	breast:

Variant related genes	Relation type
CD44	TF binding region
ENSG00000255521	Chromatin interaction
ENSG00000026508	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10488808	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs11826767	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2732575	0.88[ASN][1000 genomes]
rs2732577	0.80[ASN][1000 genomes]
rs2785173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2785179	0.88[ASN][1000 genomes]
rs353562	0.88[ASN][1000 genomes]
rs353564	0.86[ASN][1000 genomes]
rs353569	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs353575	0.88[ASN][1000 genomes]
rs353576	0.88[ASN][1000 genomes]
rs353578	0.88[ASN][1000 genomes]
rs395563	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs449670	0.88[ASN][1000 genomes]
rs497210	0.88[ASN][1000 genomes]
rs598725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60760313	0.80[ASN][1000 genomes]
rs627819	0.88[ASN][1000 genomes]
rs837512	0.80[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:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35147400-35160200	Weak transcription	Gastric	stomach
2	chr11:35149000-35158600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr11:35152400-35160000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:35152800-35159800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:35153000-35159800	Weak transcription	Primary B cells from cord blood	blood
6	chr11:35153400-35159000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr11:35153800-35156800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr11:35153800-35158400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr11:35153800-35159800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:35154000-35158800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr11:35154000-35159000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr11:35154200-35158800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr11:35154200-35159000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr11:35154200-35159000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr11:35154400-35158400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr11:35154400-35158800	Weak transcription	Primary T cells from cord blood	blood
17	chr11:35154400-35158800	Weak transcription	Dnd41	blood
18	chr11:35154400-35160200	Weak transcription	Thymus	Thymus
19	chr11:35154600-35159600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:35154600-35160000	Weak transcription	Fetal Thymus	thymus
21	chr11:35155400-35156600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:35155800-35156800	Enhancers	NHDF-Ad	bronchial
23	chr11:35155800-35156800	Enhancers	NHLF	lung
24	chr11:35156200-35156600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:35156200-35157200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:35156400-35156600	Enhancers	Stomach Smooth Muscle	stomach
27	chr11:35156400-35156800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:35156400-35156800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:35156400-35156800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:35156400-35156800	Enhancers	HSMM	muscle
31	chr11:35156400-35157000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:35156400-35157000	Enhancers	Osteobl	bone
33	chr11:35156400-35157200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:35156400-35157200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:35156400-35157400	Enhancers	Adipose Nuclei	Adipose
36	chr11:35156400-35157400	Enhancers	Small Intestine	intestine
37	chr11:35156400-35158000	Enhancers	Pancreas	Pancrea
38	chr11:35156400-35158200	Enhancers	GM12878-XiMat	blood
39	chr11:35156400-35159800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links