Variant report

Variant	rs16882540
Chromosome Location	chr5:9359641-9359642
allele	C/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	REST	chr5:9359157-9359989	H1-neurons	neurons:	n/a	n/a
2	GATA3	chr5:9359228-9359905	SK-N-SH	brain:	n/a	chr5:9359678-9359687
3	FOS	chr5:9359514-9359855	MCF10A-Er-Src	breast:	n/a	chr5:9359676-9359686 chr5:9359677-9359685 chr5:9359676-9359686
4	JUND	chr5:9359423-9359841	SK-N-SH	brain:	n/a	chr5:9359676-9359686 chr5:9359677-9359685 chr5:9359676-9359686
5	STAT3	chr5:9359467-9359847	MCF10A-Er-Src	breast:	n/a	chr5:9359609-9359617
6	TCF12	chr5:9359375-9359771	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr5:9359342-9359888	SK-N-SH	brain:	n/a	n/a
8	FOS	chr5:9359494-9359869	MCF10A-Er-Src	breast:	n/a	chr5:9359676-9359686 chr5:9359677-9359685 chr5:9359676-9359686
9	CEBPB	chr5:9359519-9359878	IMR90	lung:	n/a	n/a
10	FOS	chr5:9359506-9359825	MCF10A-Er-Src	breast:	n/a	chr5:9359676-9359686 chr5:9359677-9359685 chr5:9359676-9359686
11	FOS	chr5:9359516-9360049	MCF10A-Er-Src	breast:	n/a	chr5:9359676-9359686 chr5:9359677-9359685 chr5:9359676-9359686
12	STAT3	chr5:9359562-9359777	MCF10A-Er-Src	breast:	n/a	chr5:9359609-9359617
13	GATA3	chr5:9359434-9359922	SK-N-SH	brain:	n/a	chr5:9359678-9359687
14	TCF12	chr5:9359403-9359969	SK-N-SH	brain:	n/a	n/a
15	MYC	chr5:9359641-9359824	MCF10A-Er-Src	breast:	n/a	chr5:9359676-9359685
16	FOSL2	chr5:9359416-9359890	SK-N-SH	brain:	n/a	chr5:9359676-9359686 chr5:9359677-9359685 chr5:9359676-9359686
17	STAT3	chr5:9359523-9359847	MCF10A-Er-Src	breast:	n/a	chr5:9359609-9359617
18	STAT3	chr5:9359472-9359863	MCF10A-Er-Src	breast:	n/a	chr5:9359609-9359617
19	REST	chr5:9359313-9359784	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr5:9359445-9359769	H1-neurons	neurons:	n/a	n/a
21	STAT3	chr5:9359454-9359851	MCF10A-Er-Src	breast:	n/a	chr5:9359609-9359617
22	EP300	chr5:9359297-9359871	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr5:9359446-9359729	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:9359610..9360436-chr5:9498725..9499308,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248537	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10213796	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10213797	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10491235	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1528057	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16882525	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16882530	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16882547	1.00[YRI][hapmap];0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1020815	chr5:9135207-9425649	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv498044	chr5:9143754-9402870	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv530183	chr5:9146506-9413373	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
17	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
19	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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
20	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9332800-9372400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:9347000-9365600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:9354800-9360000	Weak transcription	Esophagus	oesophagus
4	chr5:9355200-9370200	Weak transcription	Pancreas	Pancrea
5	chr5:9356400-9360400	Enhancers	Fetal Heart	heart
6	chr5:9356600-9360000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:9357200-9377800	Weak transcription	Fetal Intestine Large	intestine
8	chr5:9357800-9363200	Weak transcription	Brain Hippocampus Middle	brain
9	chr5:9357800-9365800	Weak transcription	Brain Germinal Matrix	brain
10	chr5:9358000-9389400	Weak transcription	Brain Substantia Nigra	brain
11	chr5:9358200-9359800	Enhancers	NHLF	lung
12	chr5:9358600-9360000	Enhancers	Osteobl	bone
13	chr5:9358600-9360200	Enhancers	NH-A	brain
14	chr5:9358600-9360400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:9358600-9361800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:9358600-9362000	Weak transcription	Fetal Muscle Leg	muscle
17	chr5:9358800-9359800	Enhancers	HMEC	breast
18	chr5:9358800-9359800	Enhancers	NHDF-Ad	bronchial
19	chr5:9358800-9359800	Enhancers	NHEK	skin
20	chr5:9358800-9360400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:9358800-9363400	Weak transcription	Fetal Stomach	stomach
22	chr5:9358800-9369000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:9358800-9372400	Weak transcription	Fetal Intestine Small	intestine
24	chr5:9359000-9359800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:9359000-9359800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:9359000-9359800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:9359000-9360000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:9359000-9360200	Enhancers	Muscle Satellite Cultured Cells	--
29	chr5:9359200-9359800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:9359200-9361600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:9359200-9365800	Weak transcription	Left Ventricle	heart
32	chr5:9359200-9382800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr5:9359400-9359800	Enhancers	Fetal Kidney	kidney
34	chr5:9359400-9360400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:9359400-9361800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:9359400-9362400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr5:9359400-9363400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:9359600-9360200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr5:9359600-9361600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:9359600-9361800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr5:9359600-9363800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:9359600-9372400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links