Variant report

Variant	rs10992623
Chromosome Location	chr9:95830648-95830649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:53300638..53302382-chr9:95828777..95831211,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170421	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10821063	0.87[ASN][1000 genomes]
rs10992622	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1131773	0.89[CHD][hapmap]
rs12375973	0.86[CHD][hapmap]
rs12555029	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4077176	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4077177	0.81[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4077637	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4077811	0.92[CHD][hapmap];0.92[JPT][hapmap]
rs4078501	0.92[GIH][hapmap];0.92[JPT][hapmap]
rs4341217	0.89[CHD][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs4636265	0.85[CHD][hapmap]
rs56000948	0.93[ASN][1000 genomes]
rs57327517	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60671060	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479448	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7019574	0.86[ASN][1000 genomes]
rs7025686	0.93[ASW][hapmap];0.89[CHD][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap]
rs7036869	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7046192	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7859109	0.93[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7870697	0.93[ASN][1000 genomes]
rs7870953	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9696357	0.86[CHD][hapmap]

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	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer 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 target site	22 gene(s)	inside rSNPs	diseases
3	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv893575	chr9:95781040-95854013	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
7	nsv893577	chr9:95812707-95872216	Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv893578	chr9:95818641-95887320	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10992623	IARS	cis	parietal	SCAN
rs10992623	ASPN	cis	parietal	SCAN
rs10992623	ZNF479	trans	parietal	SCAN
rs10992623	ZNF484	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95822000-95834200	Weak transcription	Esophagus	oesophagus
2	chr9:95822000-95834200	Weak transcription	Right Atrium	heart
3	chr9:95822600-95834400	Weak transcription	Brain Hippocampus Middle	brain
4	chr9:95822800-95831000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr9:95824000-95833800	Weak transcription	Ovary	ovary
6	chr9:95824600-95854000	Weak transcription	Gastric	stomach
7	chr9:95824800-95833200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr9:95825200-95834000	Weak transcription	Liver	Liver
9	chr9:95827600-95831400	Weak transcription	GM12878-XiMat	blood
10	chr9:95827600-95831800	Genic enhancers	Primary T cells from cord blood	blood
11	chr9:95827600-95833600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
12	chr9:95827600-95839800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
13	chr9:95828000-95834200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:95828200-95830800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:95828200-95834400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:95828200-95841600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr9:95828400-95830800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr9:95828400-95833400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr9:95828400-95833800	Weak transcription	Spleen	Spleen
20	chr9:95828400-95834600	Weak transcription	Adipose Nuclei	Adipose
21	chr9:95828400-95834600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:95828400-95834600	Weak transcription	Fetal Intestine Small	intestine
23	chr9:95828400-95834600	Weak transcription	Lung	lung
24	chr9:95828400-95840000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr9:95828600-95832200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr9:95828600-95840000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr9:95828600-95845000	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr9:95828800-95832400	Weak transcription	Fetal Thymus	thymus
29	chr9:95828800-95833400	Weak transcription	Primary B cells from cord blood	blood
30	chr9:95829400-95831400	Weak transcription	Thymus	Thymus
31	chr9:95829400-95834200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr9:95829600-95831800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr9:95829600-95832200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr9:95829600-95834400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr9:95829800-95833400	Weak transcription	K562	blood
36	chr9:95830000-95832600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr9:95830200-95831400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:95830400-95830800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr9:95830400-95831400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr9:95830600-95831000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:95830600-95831000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr9:95830600-95831800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr9:95830600-95840200	Weak transcription	Primary hematopoietic stem cells	blood

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