Variant report

Variant	rs10182333
Chromosome Location	chr2:112841856-112841857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:112820549..112822093-chr2:112840179..112842837,2	K562	blood:
2	chr2:112812932..112814552-chr2:112839261..112842122,3	MCF-7	breast:
3	chr2:112831943..112834066-chr2:112841080..112842997,2	MCF-7	breast:
4	chr2:112822054..112823664-chr2:112839537..112842253,2	K562	blood:

Variant related genes	Relation type
ENSG00000153214	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10165845	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175143	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178449	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045300	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779884	0.97[ASN][1000 genomes]
rs10864898	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618637	0.90[ASN][1000 genomes]
rs4241121	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4257409	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4613287	0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4848993	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849007	0.87[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849044	0.90[ASN][1000 genomes]
rs6707397	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs6730057	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731563	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737707	0.86[CHD][hapmap];0.83[MEX][hapmap]
rs7577442	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7580507	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581849	0.90[JPT][hapmap]
rs7591702	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595574	0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308669	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653401	0.94[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653422	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][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	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10182333	CCDC138	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112814200-112849800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:112814200-112859800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:112814800-112842000	Weak transcription	Fetal Heart	heart
4	chr2:112816600-112866200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:112816800-112871400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:112820400-112847000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:112821400-112849600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:112822200-112854400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:112822800-112876800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:112823600-112844200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:112824200-112844000	Weak transcription	Fetal Brain Male	brain
12	chr2:112827200-112842600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:112829600-112850400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:112829800-112844200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:112831000-112849600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:112831800-112844000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:112831800-112850800	Strong transcription	Placenta	Placenta
18	chr2:112832000-112866000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:112833200-112842800	Weak transcription	Small Intestine	intestine
20	chr2:112833600-112845200	Weak transcription	A549	lung
21	chr2:112833600-112855800	Weak transcription	Hela-S3	cervix
22	chr2:112833800-112844200	Strong transcription	GM12878-XiMat	blood
23	chr2:112833800-112849600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:112834200-112842400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:112834200-112845200	Weak transcription	Stomach Mucosa	stomach
26	chr2:112834600-112844600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:112834600-112871200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr2:112834800-112849200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:112834800-112852200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr2:112835200-112844000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr2:112835200-112844200	Strong transcription	Primary B cells from cord blood	blood
32	chr2:112835200-112844800	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:112835200-112849000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:112835200-112851000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:112835200-112851000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:112835200-112852200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:112835400-112844000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:112835600-112850600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:112835800-112843400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:112835800-112849400	Strong transcription	HSMM	muscle
41	chr2:112835800-112883200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:112836000-112848400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:112836000-112874400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:112836400-112844000	Weak transcription	Right Ventricle	heart
45	chr2:112837000-112842200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr2:112838000-112849200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:112838000-112850400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:112838200-112842800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:112838200-112845600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr2:112838200-112846600	Strong transcription	HUVEC	blood vessel

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