Variant report

Variant	rs10123520
Chromosome Location	chr9:19051968-19051969
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:19050026..19052622-chr9:19058219..19060617,2	K562	blood:
2	chr9:19051025..19055237-chr9:19064013..19066512,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147874	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10123400	0.85[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs10125646	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1048169	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs10511670	0.84[CHB][hapmap]
rs10511671	0.84[CHB][hapmap]
rs10811110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10811112	0.84[CHB][hapmap]
rs10963943	0.88[CHB][hapmap]
rs10963953	0.84[CHB][hapmap]
rs10963955	0.83[CHB][hapmap]
rs10963962	0.84[CHB][hapmap]
rs10963964	0.84[CHB][hapmap]
rs11515236	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1154672	0.92[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1154673	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs12164262	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13287117	0.81[ASN][1000 genomes]
rs13287517	0.81[ASN][1000 genomes]
rs13302453	0.90[CHB][hapmap]
rs16937320	0.84[CHB][hapmap]
rs2291502	0.84[CHB][hapmap]
rs3780221	0.84[CHB][hapmap]
rs4392990	0.92[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4394488	0.80[ASN][1000 genomes]
rs4977490	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs4977492	0.92[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs6475311	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs6475314	0.80[ASN][1000 genomes]
rs6475315	0.92[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7022576	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs7027346	0.92[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7031392	0.83[CHB][hapmap]
rs7034297	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7034299	0.90[ASN][1000 genomes]
rs7037772	0.80[ASN][1000 genomes]
rs7037787	0.80[ASN][1000 genomes]
rs7045844	0.92[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7467137	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7854858	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7856768	0.81[ASN][1000 genomes]
rs7859259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7865126	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv973452	chr9:19033958-19053096	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19048800-19052000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:19048800-19052000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr9:19049000-19052000	Active TSS	Osteobl	bone
4	chr9:19049800-19052000	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr9:19050000-19052000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr9:19050000-19052000	Flanking Active TSS	Brain Angular Gyrus	brain
7	chr9:19050200-19052000	Flanking Active TSS	Brain Cingulate Gyrus	brain
8	chr9:19050200-19052000	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr9:19050400-19052000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:19050600-19052000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:19050600-19052000	Flanking Active TSS	Dnd41	blood
12	chr9:19050600-19052800	Flanking Active TSS	Fetal Brain Female	brain
13	chr9:19050600-19056600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:19050600-19060800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:19050600-19062600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:19050600-19063600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:19050600-19069000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:19050800-19052000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:19050800-19052000	Enhancers	Stomach Mucosa	stomach
20	chr9:19050800-19052200	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr9:19050800-19052400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:19050800-19052600	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
23	chr9:19050800-19052600	Enhancers	Small Intestine	intestine
24	chr9:19050800-19074200	Weak transcription	Lung	lung
25	chr9:19051000-19052000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr9:19051000-19052000	Flanking Active TSS	Fetal Heart	heart
27	chr9:19051000-19052000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr9:19051000-19052000	Flanking Active TSS	NHEK	skin
29	chr9:19051000-19052400	Enhancers	Primary B cells from cord blood	blood
30	chr9:19051000-19052400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr9:19051000-19052600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr9:19051000-19053400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr9:19051000-19056600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:19051000-19059000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr9:19051200-19052000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:19051200-19052000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:19051200-19052000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:19051200-19052000	Flanking Active TSS	GM12878-XiMat	blood
39	chr9:19051200-19052000	Flanking Active TSS	HepG2	liver
40	chr9:19051200-19052400	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr9:19051200-19052400	Enhancers	K562	blood
42	chr9:19051200-19052600	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr9:19051200-19057000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr9:19051400-19052000	Enhancers	Primary T cells from cord blood	blood
45	chr9:19051400-19052000	Enhancers	Colon Smooth Muscle	Colon
46	chr9:19051400-19052000	Active TSS	Right Ventricle	heart
47	chr9:19051400-19052200	Enhancers	Ovary	ovary
48	chr9:19051400-19052400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr9:19051400-19052400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr9:19051400-19052400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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