Variant report

Variant	rs13355936
Chromosome Location	chr5:99873120-99873121
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	POLR2A	chr5:99872834-99873577	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:99872854..99874470-chr5:99877624..99879735,2	K562	blood:
2	chr5:99871520..99873605-chr5:99874648..99876676,2	MCF-7	breast:
3	chr5:99870165..99872574-chr5:99872902..99874413,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247877	TF binding region
ENSG00000247877	Chromatin interaction
ENSG00000174132	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10035594	0.86[EUR][1000 genomes]
rs10036134	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10042987	0.86[EUR][1000 genomes]
rs10050943	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10065274	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10065426	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10065988	1.00[EUR][1000 genomes]
rs10072409	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10076560	0.88[EUR][1000 genomes]
rs12719287	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13355293	1.00[EUR][1000 genomes]
rs13359645	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13361748	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13436095	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17157336	0.95[EUR][1000 genomes]
rs2035118	0.88[EUR][1000 genomes]
rs3088366	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4307066	0.88[EUR][1000 genomes]
rs4995095	0.88[EUR][1000 genomes]
rs898765	0.88[EUR][1000 genomes]
rs9327193	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9327194	0.86[EUR][1000 genomes]
rs9327203	0.86[EUR][1000 genomes]
rs989981	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759359	chr5:99207674-99883371	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv2757124	chr5:99424756-99883371	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv599165	chr5:99469004-100063039	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv948969	chr5:99534096-100133827	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv882461	chr5:99745767-99927338	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv882462	chr5:99745767-100060150	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv1025132	chr5:99745775-99896429	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1025890	chr5:99745775-99936186	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1017420	chr5:99745775-100133140	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv537825	chr5:99745775-100133140	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv882463	chr5:99784116-99898851	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv882464	chr5:99784116-99905367	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv882465	chr5:99784116-99927338	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1018395	chr5:99827242-100003207	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:99870000-99874000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:99870200-99873800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:99870400-99873600	Active TSS	NHEK	skin
4	chr5:99871600-99873200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:99871800-99874400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr5:99871800-99886400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:99871800-99886400	Weak transcription	Lung	lung
8	chr5:99871800-99886800	Weak transcription	Pancreas	Pancrea
9	chr5:99871800-99889400	Weak transcription	Spleen	Spleen
10	chr5:99871800-99890200	Weak transcription	Gastric	stomach
11	chr5:99872000-99873600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:99872000-99873600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:99872000-99873800	Enhancers	Brain Substantia Nigra	brain
14	chr5:99872000-99873800	Weak transcription	Stomach Mucosa	stomach
15	chr5:99872000-99875000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr5:99872000-99881800	Weak transcription	Left Ventricle	heart
17	chr5:99872200-99873800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr5:99872200-99874200	Enhancers	Fetal Brain Male	brain
19	chr5:99872200-99875000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr5:99872400-99873400	Enhancers	Fetal Intestine Large	intestine
21	chr5:99872400-99873400	Enhancers	Fetal Stomach	stomach
22	chr5:99872400-99873600	Enhancers	Brain Germinal Matrix	brain
23	chr5:99872400-99873800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:99872400-99874000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:99872400-99874600	Enhancers	Rectal Smooth Muscle	rectum
26	chr5:99872400-99874800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr5:99872400-99875000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:99872400-99875800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr5:99872400-99876600	Weak transcription	Esophagus	oesophagus
30	chr5:99872400-99886200	Weak transcription	Small Intestine	intestine
31	chr5:99872400-99931400	Weak transcription	Aorta	Aorta
32	chr5:99872600-99873200	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr5:99872600-99873200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr5:99872600-99873400	Enhancers	Primary T cells from cord blood	blood
35	chr5:99872600-99873400	Enhancers	Primary hematopoietic stem cells	blood
36	chr5:99872600-99873400	Active TSS	Fetal Muscle Leg	muscle
37	chr5:99872600-99873400	Enhancers	Hela-S3	cervix
38	chr5:99872600-99873400	Enhancers	NH-A	brain
39	chr5:99872600-99873800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:99872600-99874000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr5:99872600-99874000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr5:99872600-99874000	Enhancers	Liver	Liver
43	chr5:99872600-99881800	Weak transcription	Right Atrium	heart
44	chr5:99872600-99886400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:99872600-99922800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:99872800-99873200	Weak transcription	Fetal Kidney	kidney
47	chr5:99872800-99873200	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr5:99872800-99873600	Weak transcription	Brain Angular Gyrus	brain
49	chr5:99872800-99873800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:99872800-99873800	Weak transcription	Primary monocytes fromperipheralblood	blood

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