Variant report

Variant	rs1864202
Chromosome Location	chr9:93601955-93601956
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:93562704..93564594-chr9:93601013..93602789,2	MCF-7	breast:
2	chr9:93595760..93597786-chr9:93599471..93602045,2	MCF-7	breast:
3	chr9:93562170..93565767-chr9:93598280..93603069,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165025	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10821511	0.83[ASN][1000 genomes]
rs10993707	0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs10993711	0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12380445	0.81[ASN][1000 genomes]
rs17489429	0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1870660	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs1993704	0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2259147	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2387337	0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2387339	0.83[ASN][1000 genomes]
rs3789898	0.83[ASN][1000 genomes]
rs3789899	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv893567	chr9:93519280-93609668	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1038685	chr9:93556174-93685729	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1039761	chr9:93598856-93677831	Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1039326	chr9:93598856-93685729	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1864202	FGD3	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93565000-93609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:93577800-93606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:93580800-93603400	Weak transcription	K562	blood
4	chr9:93585600-93607800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:93589200-93606000	Weak transcription	Colonic Mucosa	Colon
6	chr9:93591000-93603200	Weak transcription	Fetal Kidney	kidney
7	chr9:93592600-93602200	Weak transcription	Esophagus	oesophagus
8	chr9:93593600-93603400	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr9:93594200-93602800	Genic enhancers	Primary B cells from cord blood	blood
10	chr9:93595800-93603200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:93595800-93603200	Weak transcription	NHEK	skin
12	chr9:93595800-93606600	Weak transcription	Stomach Mucosa	stomach
13	chr9:93596000-93607600	Weak transcription	Fetal Intestine Large	intestine
14	chr9:93596600-93602000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:93596800-93602200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:93598000-93602200	Weak transcription	Lung	lung
17	chr9:93598000-93603200	Weak transcription	Pancreas	Pancrea
18	chr9:93598200-93606600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:93599200-93616600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:93599400-93602600	Genic enhancers	Primary monocytes fromperipheralblood	blood
21	chr9:93599600-93602000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr9:93599600-93602000	Enhancers	GM12878-XiMat	blood
23	chr9:93599600-93602400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:93599600-93602600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:93599600-93602600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr9:93599600-93602600	Strong transcription	Fetal Intestine Small	intestine
27	chr9:93599600-93602600	Genic enhancers	Monocytes-CD14+_RO01746	blood
28	chr9:93599800-93603400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:93600200-93602600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr9:93600200-93606400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr9:93600200-93613800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr9:93600800-93602200	Enhancers	Thymus	Thymus
33	chr9:93600800-93602400	Enhancers	Fetal Muscle Trunk	muscle
34	chr9:93600800-93602800	Enhancers	Fetal Thymus	thymus
35	chr9:93601000-93603400	Weak transcription	Fetal Lung	lung
36	chr9:93601000-93603400	Weak transcription	Gastric	stomach
37	chr9:93601200-93602400	Enhancers	Primary hematopoietic stem cells	blood
38	chr9:93601200-93602800	Genic enhancers	Spleen	Spleen
39	chr9:93601400-93602200	Strong transcription	Fetal Stomach	stomach
40	chr9:93601400-93602600	Weak transcription	Fetal Muscle Leg	muscle
41	chr9:93601600-93602000	Genic enhancers	Rectal Mucosa Donor 29	rectum
42	chr9:93601600-93604800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr9:93601800-93602400	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr9:93601800-93602600	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr9:93601800-93603200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr9:93601800-93642200	Weak transcription	Rectal Smooth Muscle	rectum

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