Variant report

Variant	rs10219623
Chromosome Location	chr12:48529549-48529550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48518675..48521479-chr12:48527987..48530696,2	K562	blood:
2	chr12:48503303..48504914-chr12:48527767..48530328,2	MCF-7	breast:
3	chr12:48529206..48530822-chr12:48539347..48541084,2	MCF-7	breast:
4	chr12:48527797..48530620-chr12:48531013..48533171,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10082861	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10219645	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10467101	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs10875724	0.93[JPT][hapmap]
rs10875725	1.00[JPT][hapmap]
rs10875732	1.00[JPT][hapmap]
rs10875735	0.85[AMR][1000 genomes]
rs10875736	0.82[AMR][1000 genomes]
rs10875737	0.85[AMR][1000 genomes]
rs10875738	0.85[AMR][1000 genomes]
rs10875740	0.85[AMR][1000 genomes]
rs10875745	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875746	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[ASN][1000 genomes]
rs10875747	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10875748	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10875750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10875756	0.92[ASN][1000 genomes]
rs10875762	0.83[ASN][1000 genomes]
rs10875767	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs10875770	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs10875772	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs10875792	0.85[JPT][hapmap]
rs10875793	0.92[JPT][hapmap]
rs11168357	0.93[JPT][hapmap]
rs11168369	1.00[JPT][hapmap]
rs11168371	1.00[JPT][hapmap]
rs11168383	0.85[AMR][1000 genomes]
rs11168386	0.83[AMR][1000 genomes]
rs11168401	0.85[AMR][1000 genomes]
rs11168403	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs11168413	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11168415	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168416	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11168420	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11168421	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168422	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11168425	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11168433	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11168450	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11168459	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs11168516	0.87[JPT][hapmap]
rs11558768	0.84[ASN][1000 genomes]
rs12297004	0.85[AMR][1000 genomes]
rs12297470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12301339	0.85[AMR][1000 genomes]
rs12304476	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs12305182	0.93[JPT][hapmap]
rs12305511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12305647	0.81[ASN][1000 genomes]
rs12306290	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12306451	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs12310813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311774	0.85[AMR][1000 genomes]
rs12311953	0.85[AMR][1000 genomes]
rs12312134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12313300	0.85[AMR][1000 genomes]
rs12313404	0.83[AMR][1000 genomes]
rs12315625	0.85[AMR][1000 genomes]
rs1471997	0.86[JPT][hapmap]
rs17122620	0.85[AMR][1000 genomes]
rs17122666	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17122812	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs1859445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2012773	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2079295	0.93[JPT][hapmap]
rs2107638	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2158516	0.85[AMR][1000 genomes]
rs2228500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2269933	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2269935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2269936	1.00[JPT][hapmap]
rs2279464	0.87[JPT][hapmap]
rs2286021	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3782910	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs3782911	0.85[AMR][1000 genomes]
rs4760609	0.93[JPT][hapmap]
rs4760619	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4760622	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4760680	0.85[AMR][1000 genomes]
rs4760681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4760684	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760687	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4760689	0.92[ASN][1000 genomes]
rs4760690	0.92[ASN][1000 genomes]
rs4760695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4760696	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4760697	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs58952582	0.85[AMR][1000 genomes]
rs60106007	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60761335	0.85[AMR][1000 genomes]
rs61343568	0.89[ASN][1000 genomes]
rs61918806	0.85[AMR][1000 genomes]
rs61918809	0.80[AMR][1000 genomes]
rs61918810	0.85[AMR][1000 genomes]
rs6580659	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7135779	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs719008	0.93[JPT][hapmap]
rs725454	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7299135	0.93[JPT][hapmap]
rs7299271	0.93[JPT][hapmap]
rs73102065	0.85[AMR][1000 genomes]
rs73102067	0.82[AMR][1000 genomes]
rs7485355	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7486424	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8804	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs886588	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs9634261	0.87[JPT][hapmap]
rs989144	1.00[JPT][hapmap];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv558790	chr12:48529168-48539888	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10219623	RP1-228P16.1	cis	Artery Tibial	GTEx
rs10219623	RP1-228P16.1	cis	Thyroid	GTEx
rs10219623	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48514000-48536600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr12:48514000-48537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:48515600-48535600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr12:48515800-48535600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:48515800-48545600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:48516200-48529600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:48516200-48545400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:48516200-48547200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:48516400-48529600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:48516400-48535600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:48516400-48535800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:48516400-48542000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:48516400-48545000	Strong transcription	GM12878-XiMat	blood
14	chr12:48516400-48545400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:48516400-48545800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:48516400-48547200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:48516400-48547200	Strong transcription	Stomach Smooth Muscle	stomach
18	chr12:48516400-48547800	Strong transcription	Fetal Stomach	stomach
19	chr12:48516600-48536600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:48516600-48543200	Weak transcription	Stomach Mucosa	stomach
21	chr12:48516600-48545400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:48516600-48545600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:48516800-48530400	Strong transcription	Osteobl	bone
24	chr12:48516800-48547400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:48517200-48529600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:48517600-48547400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:48518200-48529800	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr12:48518600-48547600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:48519600-48547200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr12:48519800-48529800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:48520000-48545600	Strong transcription	Hela-S3	cervix
32	chr12:48520600-48529600	Strong transcription	HSMM	muscle
33	chr12:48520600-48529800	Strong transcription	Brain Germinal Matrix	brain
34	chr12:48520800-48547400	Strong transcription	Fetal Brain Female	brain
35	chr12:48521400-48529600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr12:48522400-48534400	Weak transcription	NHDF-Ad	bronchial
37	chr12:48522600-48529600	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr12:48522600-48532800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:48522800-48530200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:48523200-48529800	Strong transcription	Fetal Intestine Large	intestine
41	chr12:48523400-48529600	Strong transcription	Brain Angular Gyrus	brain
42	chr12:48523400-48546600	Strong transcription	Fetal Muscle Leg	muscle
43	chr12:48523800-48530000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:48523800-48540400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:48523800-48547400	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:48524000-48529600	Strong transcription	NH-A	brain
47	chr12:48524000-48536400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr12:48524800-48529600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:48524800-48529600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:48525000-48529600	Strong transcription	Duodenum Mucosa	Duodenum

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