Variant report

Variant	rs13235865
Chromosome Location	chr7:5031771-5031772
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	POLR2A	chr7:5031369-5031795	HepG2	liver:	n/a	n/a
2	POLR2A	chr7:5031471-5032076	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:5031528-5031945	K562	blood:	n/a	n/a

Variant related genes	Relation type
RNF216P1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11979787	0.80[CHB][hapmap]
rs12668616	0.84[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs12668748	0.84[CHD][hapmap]
rs12670920	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12673134	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12674330	0.84[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs13233801	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13234950	0.83[AMR][1000 genomes]
rs34544476	0.84[AMR][1000 genomes]
rs34679788	0.81[EUR][1000 genomes]
rs34823543	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34841357	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35801949	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36046535	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3924252	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4073330	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4613891	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62444279	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62444280	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62444314	0.83[AMR][1000 genomes]
rs9690559	0.84[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529538	chr7:4509189-5151503	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv8033	chr7:4802287-5086597	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1022678	chr7:4810626-5113387	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv538705	chr7:4810626-5113387	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1021170	chr7:4831361-5058033	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv538706	chr7:4831361-5058033	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1033855	chr7:4862677-5069764	Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
12	nsv1019120	chr7:4929653-5138409	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
13	nsv917078	chr7:4962123-5151633	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv525289	chr7:5003373-5083741	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 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	chr7:5014600-5036200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:5014600-5041000	Weak transcription	Stomach Mucosa	stomach
3	chr7:5014800-5040000	Weak transcription	Right Atrium	heart
4	chr7:5014800-5041400	Weak transcription	Fetal Heart	heart
5	chr7:5015800-5039200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:5015800-5041800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:5016000-5038200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:5016000-5042000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:5016200-5038400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:5016200-5039000	Strong transcription	Liver	Liver
11	chr7:5016600-5040000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:5017600-5033200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:5017800-5045400	Weak transcription	Fetal Brain Male	brain
14	chr7:5018200-5041800	Strong transcription	Dnd41	blood
15	chr7:5020600-5039000	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr7:5022200-5039600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:5022800-5039000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr7:5023000-5034600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:5023200-5039600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr7:5023400-5038800	Strong transcription	Osteobl	bone
21	chr7:5023400-5039200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:5023400-5040000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr7:5023600-5037400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr7:5023600-5038000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:5023600-5039200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr7:5023600-5039200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr7:5023600-5039200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr7:5023800-5031800	Strong transcription	A549	lung
29	chr7:5023800-5037200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr7:5023800-5037800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:5023800-5038000	Strong transcription	Fetal Lung	lung
32	chr7:5023800-5038200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr7:5023800-5038400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr7:5023800-5038800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:5023800-5039000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr7:5023800-5039200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:5023800-5039200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr7:5023800-5039200	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:5023800-5040000	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr7:5023800-5042200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr7:5024000-5037600	Strong transcription	Primary B cells from cord blood	blood
42	chr7:5024000-5038800	Strong transcription	Brain Hippocampus Middle	brain
43	chr7:5024000-5039600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr7:5024000-5039600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr7:5024000-5039600	Strong transcription	Stomach Smooth Muscle	stomach
46	chr7:5024000-5040200	Strong transcription	Adipose Nuclei	Adipose
47	chr7:5024200-5038800	Strong transcription	Fetal Intestine Large	intestine
48	chr7:5024200-5040200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:5024400-5032200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr7:5024400-5036600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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