Variant report

Variant	rs9873904
Chromosome Location	chr3:178869413-178869414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178781504..178783011-chr3:178869309..178871100,2	K562	blood:
2	chr3:178869093..178870734-chr3:178895152..178896697,2	K562	blood:
3	chr3:178866930..178870480-chr3:178976906..178979282,3	K562	blood:
4	chr15:65595682..65597478-chr3:178866855..178869442,2	MCF-7	breast:
5	chr3:178867742..178870161-chr3:178876132..178878163,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240429	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000171121	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12330454	0.87[AMR][1000 genomes]
rs28419257	0.87[AMR][1000 genomes]
rs6804779	0.87[AMR][1000 genomes]
rs9811268	1.00[AFR][1000 genomes]
rs9831927	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription 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	22 gene(s)	inside rSNPs	diseases
7	nsv878037	chr3:178825910-178871906	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178867200-178878200	Weak transcription	Gastric	stomach
2	chr3:178867600-178869600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:178867600-178870600	Enhancers	Fetal Heart	heart
4	chr3:178867600-178872000	Weak transcription	Esophagus	oesophagus
5	chr3:178867600-178872000	Weak transcription	Left Ventricle	heart
6	chr3:178867600-178878200	Weak transcription	Pancreas	Pancrea
7	chr3:178867600-178882400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:178867600-178883400	Weak transcription	Stomach Mucosa	stomach
9	chr3:178867800-178869600	Enhancers	Brain Hippocampus Middle	brain
10	chr3:178867800-178869800	Enhancers	Primary B cells from peripheral blood	blood
11	chr3:178867800-178869800	Enhancers	Liver	Liver
12	chr3:178867800-178870600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:178867800-178870600	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr3:178867800-178871000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:178867800-178873600	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:178867800-178874000	Weak transcription	Fetal Stomach	stomach
17	chr3:178867800-178878000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:178867800-178878200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:178867800-178878200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:178867800-178900200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:178868000-178869600	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr3:178868000-178869600	Enhancers	Brain Anterior Caudate	brain
23	chr3:178868000-178869600	Enhancers	Thymus	Thymus
24	chr3:178868000-178869800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:178868000-178869800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:178868000-178869800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:178868000-178869800	Enhancers	Adipose Nuclei	Adipose
28	chr3:178868000-178869800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr3:178868000-178869800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr3:178868000-178870200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr3:178868000-178870400	Enhancers	HepG2	liver
32	chr3:178868000-178870600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:178868000-178870600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr3:178868000-178870800	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr3:178868000-178870800	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr3:178868000-178871400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:178868000-178871800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:178868000-178874200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:178868000-178878200	Weak transcription	Right Atrium	heart
40	chr3:178868000-178892400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:178868200-178869600	Enhancers	Fetal Brain Female	brain
42	chr3:178868200-178869800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:178868200-178869800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:178868200-178869800	Enhancers	Fetal Kidney	kidney
45	chr3:178868200-178871400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr3:178868400-178869600	Active TSS	GM12878-XiMat	blood
47	chr3:178868400-178876000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr3:178868600-178869600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:178868600-178869600	Enhancers	HUVEC	blood vessel
50	chr3:178868600-178869800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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