Variant report

Variant	rs290213
Chromosome Location	chr9:93595807-93595808
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:93589349..93592337-chr9:93594692..93596679,2	MCF-7	breast:
2	chr9:93595760..93597786-chr9:93599471..93602045,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165025	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1172988	1.00[ASN][1000 genomes]
rs1172989	1.00[ASN][1000 genomes]
rs11794023	1.00[ASN][1000 genomes]
rs12377938	1.00[ASN][1000 genomes]
rs12551863	1.00[ASN][1000 genomes]
rs158508	1.00[CHB][hapmap]
rs1675317	1.00[ASN][1000 genomes]
rs1755958	1.00[CHB][hapmap]
rs1760124	1.00[CHB][hapmap]
rs2035072	1.00[CHB][hapmap]
rs209424	1.00[ASN][1000 genomes]
rs209971	1.00[ASN][1000 genomes]
rs2613310	1.00[CHB][hapmap]
rs2613320	1.00[CHB][hapmap]
rs290220	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs290225	1.00[CHB][hapmap]
rs290232	1.00[CHB][hapmap]
rs290234	1.00[CHB][hapmap]
rs290235	1.00[CHB][hapmap]
rs290236	1.00[CHB][hapmap]
rs290237	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs290238	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs290244	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290256	1.00[CHB][hapmap]
rs290261	1.00[ASN][1000 genomes]
rs290262	1.00[ASN][1000 genomes]
rs290264	1.00[ASN][1000 genomes]
rs290272	1.00[ASN][1000 genomes]
rs290277	1.00[ASN][1000 genomes]
rs290983	1.00[ASN][1000 genomes]
rs291002	1.00[ASN][1000 genomes]
rs291004	1.00[ASN][1000 genomes]
rs291007	1.00[ASN][1000 genomes]
rs4744493	1.00[ASN][1000 genomes]
rs4744496	1.00[ASN][1000 genomes]
rs56049925	1.00[ASN][1000 genomes]
rs72731311	1.00[ASN][1000 genomes]
rs72731312	1.00[ASN][1000 genomes]
rs965892	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs290213	SHC3	cis	parietal	SCAN

Chromatin state (count:38 , 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	chr9:93567800-93597400	Weak transcription	Gastric	stomach
3	chr9:93577000-93598800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:93577800-93606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:93580800-93603400	Weak transcription	K562	blood
6	chr9:93583000-93599600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr9:93585600-93607800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:93589200-93606000	Weak transcription	Colonic Mucosa	Colon
9	chr9:93590000-93601600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:93591000-93599600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr9:93591000-93603200	Weak transcription	Fetal Kidney	kidney
12	chr9:93591200-93596400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:93591800-93596400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr9:93592600-93602200	Weak transcription	Esophagus	oesophagus
15	chr9:93593200-93596000	Enhancers	Fetal Intestine Small	intestine
16	chr9:93593600-93596800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr9:93593600-93597200	Weak transcription	Pancreas	Pancrea
18	chr9:93593600-93603400	Genic enhancers	Primary B cells from peripheral blood	blood
19	chr9:93594000-93596800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:93594200-93596200	Enhancers	GM12878-XiMat	blood
21	chr9:93594200-93602800	Genic enhancers	Primary B cells from cord blood	blood
22	chr9:93594400-93596200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr9:93594600-93596000	Enhancers	Fetal Intestine Large	intestine
24	chr9:93594600-93596800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:93594600-93597200	Strong transcription	Primary hematopoietic stem cells	blood
26	chr9:93595000-93596200	Enhancers	Small Intestine	intestine
27	chr9:93595000-93596800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr9:93595200-93597800	Strong transcription	Thymus	Thymus
29	chr9:93595400-93596800	Weak transcription	Fetal Thymus	thymus
30	chr9:93595400-93597200	Weak transcription	Fetal Stomach	stomach
31	chr9:93595400-93597400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:93595400-93599600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:93595600-93596200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:93595600-93596600	Enhancers	Duodenum Mucosa	Duodenum
35	chr9:93595800-93596400	Weak transcription	Spleen	Spleen
36	chr9:93595800-93603200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:93595800-93603200	Weak transcription	NHEK	skin
38	chr9:93595800-93606600	Weak transcription	Stomach Mucosa	stomach

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