Variant report

Variant	rs71313590
Chromosome Location	chr3:99876489-99876490
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	EP300	chr3:99876484-99879473	SK-N-SH	brain:	n/a	chr3:99878563-99878572

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99875365..99878075-chr3:99879723..99882009,2	K562	blood:

Variant related genes	Relation type
CMSS1	TF binding region
ENSG00000184220	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13074029	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13094890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13096852	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13098066	0.86[EUR][1000 genomes]
rs35074168	0.83[EUR][1000 genomes]
rs62285469	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62285475	0.88[EUR][1000 genomes]
rs62285476	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62285480	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647466	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99856000-99877800	Weak transcription	Ovary	ovary
2	chr3:99858600-99877200	Weak transcription	HSMM	muscle
3	chr3:99864400-99886600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr3:99865000-99894600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:99865600-99898400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:99868000-99897000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr3:99869000-99895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:99869000-99897800	Weak transcription	Pancreas	Pancrea
9	chr3:99870400-99898600	Weak transcription	Esophagus	oesophagus
10	chr3:99871400-99899400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:99873600-99877800	Weak transcription	Fetal Kidney	kidney
12	chr3:99873800-99877400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:99874000-99876600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr3:99874200-99877000	ZNF genes & repeats	Fetal Muscle Leg	muscle
15	chr3:99874400-99894400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:99874400-99897000	Weak transcription	K562	blood
17	chr3:99874600-99877000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:99874600-99877000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:99874600-99877000	Weak transcription	NHDF-Ad	bronchial
20	chr3:99874600-99877200	Weak transcription	Osteobl	bone
21	chr3:99874600-99877400	Weak transcription	NHEK	skin
22	chr3:99874600-99877600	Weak transcription	Liver	Liver
23	chr3:99874600-99877600	Weak transcription	Fetal Lung	lung
24	chr3:99874600-99878400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:99874600-99879000	Weak transcription	Small Intestine	intestine
26	chr3:99874600-99885200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:99874600-99897400	Weak transcription	A549	lung
28	chr3:99874800-99877600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:99874800-99878800	Weak transcription	Primary T cells from cord blood	blood
30	chr3:99874800-99886600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:99874800-99886600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:99874800-99891000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:99874800-99895200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:99874800-99897200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:99874800-99897200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr3:99874800-99897200	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:99874800-99898200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:99874800-99898400	Weak transcription	HepG2	liver
39	chr3:99875000-99876800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:99875000-99897400	Weak transcription	GM12878-XiMat	blood
41	chr3:99875200-99877000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:99875200-99881000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:99875200-99886400	Weak transcription	Dnd41	blood
44	chr3:99875200-99886600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:99875200-99887000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr3:99875400-99877800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:99875400-99890400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:99875600-99878800	Weak transcription	Fetal Stomach	stomach
49	chr3:99875800-99876800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:99876000-99876800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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