Variant report

Variant	rs11713324
Chromosome Location	chr3:52926687-52926688
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	chr3:52925161..52929038-chr3:52929982..52933172,4	MCF-7	breast:
2	chr3:52925648..52928191-chr3:52930062..52932793,2	K562	blood:

Variant related genes	Relation type
ENSG00000213533	Chromatin interaction
ENSG00000248592	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10510761	0.87[GIH][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11130329	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1139106	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11626	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap]
rs11705797	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11707829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708337	0.93[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11708390	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710394	0.87[GIH][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11712498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713290	0.88[AFR][1000 genomes]
rs11713376	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11713479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11714793	0.93[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715498	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11716506	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11716612	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11717132	0.88[AFR][1000 genomes]
rs11717619	0.87[GIH][hapmap]
rs11717749	1.00[CHB][hapmap]
rs11718060	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11718538	0.88[AFR][1000 genomes]
rs11718834	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11720191	0.84[AFR][1000 genomes]
rs11720228	1.00[CHB][hapmap]
rs11720233	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720488	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13060282	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062228	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13067373	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13068194	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13074524	0.82[AFR][1000 genomes]
rs13076033	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13080929	0.81[CEU][hapmap]
rs13089969	1.00[ASN][1000 genomes]
rs13091844	1.00[YRI][hapmap]
rs13092352	0.88[AFR][1000 genomes]
rs13095705	0.93[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17331151	1.00[CHB][hapmap]
rs17331178	1.00[CHB][hapmap]
rs1986656	1.00[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001732	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap]
rs2240916	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs2336540	0.88[AFR][1000 genomes]
rs2336541	0.84[AFR][1000 genomes]
rs2336661	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2336665	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34026403	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34313969	0.88[AFR][1000 genomes]
rs35230793	1.00[ASN][1000 genomes]
rs35384050	0.84[AFR][1000 genomes]
rs35404467	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35569457	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35651539	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35737577	0.82[AFR][1000 genomes]
rs35849389	0.84[AFR][1000 genomes]
rs36126605	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3733034	0.86[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3733035	0.93[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3796352	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs4608686	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56231111	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58515094	0.88[AFR][1000 genomes]
rs60887045	0.88[AFR][1000 genomes]
rs60942590	0.84[AFR][1000 genomes]
rs61172708	0.88[AFR][1000 genomes]
rs61473083	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6762260	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6798472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71299621	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71299622	1.00[ASN][1000 genomes]
rs73839535	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9831977	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11713324	TMEM110	cis	cerebellum	SCAN
rs11713324	TMEM110	cis	lymphoblastoid	seeQTL
rs11713324	DNAH1	cis	parietal	SCAN
rs11713324	ITIH4	cis	parietal	SCAN
rs11713324	MUSTN1	cis	cerebellum	SCAN
rs11713324	MON1A	cis	parietal	SCAN
rs11713324	ITIH4	cis	multi-tissue	Pritchard
rs11713324	TMEM110	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
2	chr3:52908400-52930600	Weak transcription	A549	lung
3	chr3:52910000-52929400	Weak transcription	HMEC	breast
4	chr3:52910000-52930200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:52910200-52929800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:52910200-52930000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:52910200-52930000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:52910200-52930000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:52910400-52930200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:52916400-52930600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:52919200-52930200	Weak transcription	Fetal Kidney	kidney
12	chr3:52920000-52929200	Weak transcription	Dnd41	blood
13	chr3:52920200-52929400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:52920200-52929800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:52920400-52930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:52920400-52930600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:52920400-52930600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:52921600-52930600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:52921800-52927800	Weak transcription	Right Ventricle	heart
20	chr3:52923400-52927400	Enhancers	Fetal Lung	lung
21	chr3:52923800-52928800	Enhancers	Brain Cingulate Gyrus	brain
22	chr3:52924000-52927200	Enhancers	Pancreas	Pancrea
23	chr3:52924000-52929400	Enhancers	Brain Hippocampus Middle	brain
24	chr3:52924000-52930000	Enhancers	Brain Substantia Nigra	brain
25	chr3:52924200-52927200	Enhancers	Gastric	stomach
26	chr3:52924200-52930200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr3:52924400-52928400	Enhancers	Stomach Mucosa	stomach
28	chr3:52924600-52926800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:52924600-52926800	Enhancers	NHLF	lung
30	chr3:52924600-52927000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:52924600-52930200	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr3:52924800-52929600	Genic enhancers	Thymus	Thymus
33	chr3:52925000-52927800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:52925000-52928200	Weak transcription	Fetal Brain Female	brain
35	chr3:52925000-52928800	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:52925200-52926800	Enhancers	Fetal Intestine Large	intestine
37	chr3:52925200-52926800	Enhancers	Ovary	ovary
38	chr3:52925200-52926800	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr3:52925200-52927000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr3:52925200-52927000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:52925200-52928000	Enhancers	Primary B cells from peripheral blood	blood
42	chr3:52925200-52928200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr3:52925200-52928200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr3:52925200-52928400	Enhancers	Primary hematopoietic stem cells	blood
45	chr3:52925200-52928400	Flanking Active TSS	GM12878-XiMat	blood
46	chr3:52925200-52928800	Enhancers	Adipose Nuclei	Adipose
47	chr3:52925200-52929600	Genic enhancers	Fetal Thymus	thymus
48	chr3:52925400-52926800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:52925400-52927000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr3:52925400-52927000	Enhancers	Duodenum Smooth Muscle	Duodenum

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