Variant report

Variant	rs11160830
Chromosome Location	chr14:105481988-105481989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:105448840..105458160-chr14:105477229..105492100,32	MCF-7	breast:
2	chr14:105481065..105482963-chr14:105779848..105781960,2	MCF-7	breast:
3	chr14:105470658..105473658-chr14:105481762..105484641,3	K562	blood:
4	chr14:105433937..105458439-chr14:105476653..105492775,70	MCF-7	breast:
5	chr14:105329597..105332501-chr14:105481156..105484994,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140104	Chromatin interaction
ENSG00000185024	Chromatin interaction
ENSG00000099814	Chromatin interaction
ENSG00000185567	Chromatin interaction
ENSG00000179364	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10131315	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137513	0.92[ASN][1000 genomes]
rs10138381	0.93[ASN][1000 genomes]
rs10150848	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10873553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11160829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628851	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11845745	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12896131	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241867	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2247140	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2582567	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2582568	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2582569	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3204172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3204173	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923887	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075086	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4077684	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4267250	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4309336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4344668	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4354858	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4429223	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6420941	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6576065	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6576066	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6576068	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7141972	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7147450	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7150384	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7155932	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7157046	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8010080	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8011377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8016434	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8017794	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8022294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs894039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9652406	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828345	chr14:105100787-105803170	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh 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	165 gene(s)	inside rSNPs	diseases
2	nsv542225	chr14:105133688-105803170	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv542227	chr14:105157572-105803170	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
4	nsv917106	chr14:105339195-105803170	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv902419	chr14:105381763-105494262	Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv456457	chr14:105404384-105555396	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv566141	chr14:105404384-105555396	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	nsv902420	chr14:105410183-105494262	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
9	nsv902421	chr14:105410183-105574843	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
10	nsv902422	chr14:105420215-105803170	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
11	nsv1052190	chr14:105423761-105722653	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
12	nsv902423	chr14:105430890-105803170	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
13	nsv1042303	chr14:105435649-105633544	Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
14	nsv456458	chr14:105435649-105690092	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
15	nsv566150	chr14:105435649-105690092	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
16	nsv902424	chr14:105436222-105803170	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh 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	86 gene(s)	inside rSNPs	diseases
17	nsv566151	chr14:105459140-105555396	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
18	nsv456459	chr14:105459140-105617891	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
19	nsv566152	chr14:105459140-105617891	Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
20	nsv902425	chr14:105463936-105690092	Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11160830	CDCA4	cis	multi-tissue	Pritchard
rs11160830	DYNC1H1	cis	parietal	SCAN
rs11160830	KIAA0284	cis	cerebellum	SCAN
rs11160830	DIO3OS	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105453200-105485400	Weak transcription	Fetal Kidney	kidney
2	chr14:105463400-105485800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr14:105473800-105484800	Weak transcription	Primary B cells from cord blood	blood
4	chr14:105473800-105486600	Weak transcription	Aorta	Aorta
5	chr14:105474200-105482600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr14:105474800-105484800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr14:105474800-105485600	Weak transcription	Small Intestine	intestine
8	chr14:105475800-105485600	Enhancers	Fetal Heart	heart
9	chr14:105476200-105485400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr14:105477200-105483200	Genic enhancers	Fetal Stomach	stomach
11	chr14:105478000-105482200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr14:105478200-105482000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr14:105478200-105482400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr14:105478200-105482800	Weak transcription	Colonic Mucosa	Colon
15	chr14:105478200-105485400	Weak transcription	Ovary	ovary
16	chr14:105478200-105485600	Weak transcription	Liver	Liver
17	chr14:105478200-105485800	Weak transcription	Brain Angular Gyrus	brain
18	chr14:105478200-105486200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr14:105478400-105482400	Enhancers	Fetal Brain Male	brain
20	chr14:105478400-105482800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr14:105478400-105483000	Weak transcription	Placenta	Placenta
22	chr14:105478400-105483000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr14:105478400-105485400	Weak transcription	Fetal Intestine Large	intestine
24	chr14:105478400-105486200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr14:105478400-105486200	Weak transcription	Lung	lung
26	chr14:105478400-105486400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr14:105478600-105484800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr14:105478600-105485200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr14:105478800-105482000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr14:105478800-105482800	Genic enhancers	HMEC	breast
31	chr14:105478800-105483400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr14:105478800-105485400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr14:105479000-105482800	Genic enhancers	NHEK	skin
34	chr14:105479200-105483200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr14:105479200-105484400	Genic enhancers	A549	lung
36	chr14:105479400-105482000	Enhancers	NH-A	brain
37	chr14:105479400-105482800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr14:105479400-105482800	Weak transcription	Pancreas	Pancrea
39	chr14:105479400-105483000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr14:105479400-105485600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr14:105479600-105485600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr14:105479600-105486200	Weak transcription	Left Ventricle	heart
43	chr14:105479800-105483000	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr14:105479800-105483400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
45	chr14:105479800-105484200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr14:105479800-105485400	Genic enhancers	Fetal Thymus	thymus
47	chr14:105480000-105482000	Enhancers	Primary B cells from peripheral blood	blood
48	chr14:105480000-105482600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr14:105480000-105482800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr14:105480000-105484800	Weak transcription	Right Ventricle	heart

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