Variant report

Variant	rs10838663
Chromosome Location	chr11:47184971-47184972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47179475..47181210-chr11:47184967..47187078,2	MCF-7	breast:
2	chr11:47176955..47179833-chr11:47182834..47185275,2	K562	blood:
3	chr11:47184473..47185977-chr6:26123417..26125817,2	K562	blood:
4	chr11:47183385..47185292-chr17:56403714..56405426,2	K562	blood:
5	chr11:47183256..47186030-chr11:47281970..47284554,2	MCF-7	breast:
6	chr11:47183301..47185568-chr11:47370586..47372939,2	K562	blood:
7	chr11:46970587..46973185-chr11:47182326..47184987,2	MCF-7	breast:
8	chr11:46890949..46892684-chr11:47183314..47186093,2	K562	blood:
9	chr11:46912513..46914705-chr11:47182885..47185106,2	K562	blood:
10	chr11:47183888..47186311-chr11:47279921..47282394,2	MCF-7	breast:
11	chr11:47182976..47185487-chr11:47185518..47189747,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000180573	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000180596	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10466478	0.83[CHB][hapmap]
rs10501319	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs1051006	0.80[CEU][hapmap]
rs1060573	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs10742797	0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10769225	0.80[ASN][1000 genomes]
rs10769226	0.82[ASN][1000 genomes]
rs10769227	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10769228	0.83[ASN][1000 genomes]
rs10769234	0.86[CHB][hapmap]
rs10769248	0.88[ASN][1000 genomes]
rs10769253	0.80[CEU][hapmap]
rs10838640	0.82[ASN][1000 genomes]
rs10838641	0.83[ASN][1000 genomes]
rs10838644	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs10838646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10838652	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs10838658	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10838660	0.83[CHB][hapmap]
rs10838662	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10838664	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10838689	0.80[CEU][hapmap]
rs11039074	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs11039080	0.92[ASN][1000 genomes]
rs11039081	0.93[ASN][1000 genomes]
rs11039097	0.83[CHB][hapmap]
rs11039098	0.84[ASN][1000 genomes]
rs11039105	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs11039112	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs11039119	0.83[CHB][hapmap]
rs11600668	0.83[CHB][hapmap]
rs11601798	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11603373	0.95[ASN][1000 genomes]
rs12224096	0.82[CHB][hapmap]
rs12417519	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs12574410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12796744	0.83[CHB][hapmap]
rs17790204	0.81[ASN][1000 genomes]
rs1872896	0.83[CHB][hapmap]
rs2087215	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs2242261	1.00[CEU][hapmap]
rs2242262	1.00[CEU][hapmap]
rs2279238	1.00[CEU][hapmap]
rs2279438	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2279439	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2290146	0.80[CEU][hapmap]
rs2290148	0.80[CEU][hapmap]
rs2306353	1.00[CEU][hapmap]
rs2633080	1.00[CEU][hapmap]
rs2957873	0.81[MEX][hapmap]
rs3729802	0.85[CEU][hapmap]
rs3758666	0.86[ASN][1000 genomes]
rs3758667	0.82[ASN][1000 genomes]
rs3781619	1.00[CEU][hapmap]
rs3824866	1.00[CEU][hapmap]
rs3922684	0.96[ASN][1000 genomes]
rs4269876	0.96[ASN][1000 genomes]
rs4315028	0.93[ASN][1000 genomes]
rs4394802	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4494268	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.85[ASN][1000 genomes]
rs4498951	0.96[ASN][1000 genomes]
rs4528282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4548577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4576779	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4587689	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs4752815	0.80[ASN][1000 genomes]
rs4752816	0.80[ASN][1000 genomes]
rs4752951	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4752957	0.83[CHB][hapmap]
rs4752962	0.83[CHB][hapmap]
rs4752965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752967	0.83[CHB][hapmap]
rs4752968	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752969	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4752977	0.80[CEU][hapmap]
rs4752983	0.80[CEU][hapmap]
rs61896133	0.96[ASN][1000 genomes]
rs61896136	0.96[ASN][1000 genomes]
rs61897787	0.86[ASN][1000 genomes]
rs61897844	0.88[ASN][1000 genomes]
rs61897857	0.86[ASN][1000 genomes]
rs6485715	0.80[ASN][1000 genomes]
rs6485716	0.81[ASN][1000 genomes]
rs6485726	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs6485739	0.83[CHB][hapmap]
rs7103581	0.83[CHB][hapmap]
rs7108822	0.87[ASN][1000 genomes]
rs7108902	0.83[CHB][hapmap]
rs7111270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7112854	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs7114683	0.92[ASN][1000 genomes]
rs7118396	1.00[CEU][hapmap]
rs7121418	0.83[CHB][hapmap]
rs7123632	0.82[ASN][1000 genomes]
rs7124648	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs7125807	0.82[CHB][hapmap]
rs7126005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs7127741	0.92[ASN][1000 genomes]
rs7128650	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs7130006	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7130947	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7395496	1.00[CEU][hapmap]
rs747650	0.83[CHB][hapmap]
rs753992	0.80[CEU][hapmap]
rs7929688	0.80[ASN][1000 genomes]
rs7931260	0.83[CHB][hapmap]
rs7935346	0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7937410	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7938169	0.80[ASN][1000 genomes]
rs7939786	0.80[ASN][1000 genomes]
rs7940240	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7945315	0.83[CHB][hapmap]
rs7946709	0.83[CHB][hapmap]
rs7950753	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs7951979	0.95[ASN][1000 genomes]
rs830084	1.00[CEU][hapmap]
rs901747	0.95[ASN][1000 genomes]
rs923324	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10838663	PTPMT1	cis	parietal	SCAN
rs10838663	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs10838663	DDB2	Cis_1M	lymphoblastoid	RTeQTL
rs10838663	ACP2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47165000-47185000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:47165200-47185600	Weak transcription	Aorta	Aorta
3	chr11:47165400-47188600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:47171400-47186000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:47171600-47186400	Weak transcription	Psoas Muscle	Psoas
6	chr11:47174800-47185600	Weak transcription	Left Ventricle	heart
7	chr11:47175200-47185600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr11:47175200-47185600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:47175200-47185800	Weak transcription	Small Intestine	intestine
10	chr11:47175200-47186400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:47175200-47188600	Weak transcription	Fetal Heart	heart
12	chr11:47175400-47185400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:47175400-47185400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:47175400-47185600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr11:47175400-47185600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:47175400-47185600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:47175400-47186000	Weak transcription	HUVEC	blood vessel
18	chr11:47175400-47186600	Weak transcription	Fetal Kidney	kidney
19	chr11:47175400-47197600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr11:47176000-47196600	Strong transcription	Fetal Intestine Small	intestine
21	chr11:47176200-47185600	Weak transcription	HSMM	muscle
22	chr11:47176200-47187800	Weak transcription	NHDF-Ad	bronchial
23	chr11:47176600-47188600	Weak transcription	Fetal Brain Male	brain
24	chr11:47176800-47193000	Strong transcription	Fetal Brain Female	brain
25	chr11:47176800-47196600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:47177000-47186200	Weak transcription	GM12878-XiMat	blood
27	chr11:47177400-47186200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr11:47177400-47187000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr11:47177800-47185600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:47178000-47186400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr11:47178000-47186400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr11:47178000-47197000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:47178200-47194000	Strong transcription	Dnd41	blood
34	chr11:47178400-47186200	Weak transcription	HSMMtube	muscle
35	chr11:47178600-47185200	Weak transcription	HMEC	breast
36	chr11:47178800-47196800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:47180000-47185200	Weak transcription	Lung	lung
38	chr11:47180000-47186000	Weak transcription	Fetal Lung	lung
39	chr11:47180400-47185400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr11:47180600-47196600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr11:47180800-47186200	Weak transcription	Stomach Mucosa	stomach
42	chr11:47180800-47188600	Weak transcription	K562	blood
43	chr11:47181400-47197000	Weak transcription	Right Atrium	heart
44	chr11:47182000-47196400	Strong transcription	Hela-S3	cervix
45	chr11:47182200-47185600	Strong transcription	Thymus	Thymus
46	chr11:47182200-47193400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:47182200-47194800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr11:47182200-47197000	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr11:47182400-47187200	Genic enhancers	Fetal Muscle Trunk	muscle
50	chr11:47182400-47196400	Strong transcription	Fetal Intestine Large	intestine

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