Variant report

Variant	rs799466
Chromosome Location	chr14:35503326-35503327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:35500902..35503626-chr14:35810015..35811675,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10483452	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1091349	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11620951	0.83[ASN][1000 genomes]
rs11624462	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs11625046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625507	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11625810	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11626113	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs12147861	0.83[ASN][1000 genomes]
rs12881415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12882986	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12888766	0.88[YRI][hapmap]
rs12890586	0.80[ASN][1000 genomes]
rs1627716	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1712354	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1738799	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34116113	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs34319196	0.87[ASN][1000 genomes]
rs34658054	0.87[ASN][1000 genomes]
rs34844770	0.87[ASN][1000 genomes]
rs35361707	0.87[ASN][1000 genomes]
rs35468265	0.90[ASN][1000 genomes]
rs35861323	0.87[ASN][1000 genomes]
rs4432181	0.91[CHD][hapmap];0.88[YRI][hapmap]
rs55805245	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55815172	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56240056	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61989479	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61989495	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61989546	0.80[ASN][1000 genomes]
rs61989547	0.80[ASN][1000 genomes]
rs66539779	0.87[ASN][1000 genomes]
rs712305	0.90[ASN][1000 genomes]
rs712310	0.90[ASN][1000 genomes]
rs712313	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs71421926	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs799455	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799456	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];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799465	0.90[ASN][1000 genomes]
rs799467	0.84[ASW][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs799470	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs799471	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs799472	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs799475	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799481	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799482	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799485	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs799489	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs799490	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs799493	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs799494	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799496	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799663	0.90[ASN][1000 genomes]
rs799666	0.83[ASN][1000 genomes]
rs799667	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs876144	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456203	chr14:35311272-35512335	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv564200	chr14:35311272-35512335	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
3	nsv901602	chr14:35367889-35571651	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv949617	chr14:35379923-35825436	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv1043470	chr14:35398522-35754029	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
6	nsv542031	chr14:35398522-35754029	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
7	nsv901605	chr14:35409214-35512335	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv901606	chr14:35449467-35512335	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv901607	chr14:35449467-35540764	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
10	nsv901608	chr14:35449467-35571651	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
11	nsv901609	chr14:35449467-35587767	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
12	nsv456204	chr14:35466584-35556498	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv564263	chr14:35466584-35556498	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv901610	chr14:35470049-35509571	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv901611	chr14:35470049-35540764	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
16	nsv901612	chr14:35470049-35571651	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv901613	chr14:35470049-35587767	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
18	nsv1239	chr14:35477657-35522987	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
19	nsv564264	chr14:35482797-35732369	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
20	nsv901614	chr14:35485748-35571651	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
21	nsv901615	chr14:35485748-35630175	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
22	nsv870305	chr14:35488290-35852349	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
23	nsv1043801	chr14:35493065-35539399	Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs799466	KIAA0391	cis	cerebellum	SCAN
rs799466	PPP2R3C	cis	lymphoblastoid	seeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35454400-35509800	Weak transcription	Psoas Muscle	Psoas
2	chr14:35466000-35503800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr14:35467600-35503600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr14:35474400-35503400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr14:35480400-35504000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr14:35485800-35514800	Weak transcription	Right Ventricle	heart
7	chr14:35488600-35514200	Weak transcription	Small Intestine	intestine
8	chr14:35489000-35507200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr14:35490200-35514600	Weak transcription	NHLF	lung
10	chr14:35493000-35503400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr14:35493800-35503800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr14:35495600-35503400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr14:35496800-35514600	Weak transcription	HSMMtube	muscle
14	chr14:35498000-35503400	Strong transcription	Fetal Stomach	stomach
15	chr14:35498000-35514200	Weak transcription	Fetal Kidney	kidney
16	chr14:35498200-35503400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr14:35498400-35505800	Weak transcription	HSMM	muscle
18	chr14:35498600-35514600	Weak transcription	Colon Smooth Muscle	Colon
19	chr14:35499000-35503400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr14:35499000-35503400	Weak transcription	NHDF-Ad	bronchial
21	chr14:35499800-35503400	Strong transcription	Primary T cells from cord blood	blood
22	chr14:35499800-35504000	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr14:35500200-35504200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr14:35500400-35514200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr14:35500600-35503400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr14:35500600-35503600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr14:35501000-35504000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr14:35501200-35503400	Weak transcription	Gastric	stomach
29	chr14:35501200-35503800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr14:35501400-35503400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr14:35501600-35504000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr14:35501800-35503400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr14:35501800-35503400	Strong transcription	Brain Anterior Caudate	brain
34	chr14:35501800-35503800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
35	chr14:35501800-35503800	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr14:35501800-35514400	Weak transcription	NH-A	brain
37	chr14:35502000-35503400	Weak transcription	Pancreas	Pancrea
38	chr14:35502000-35503600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr14:35502000-35504000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
40	chr14:35502200-35503400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr14:35502200-35503800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr14:35502200-35504600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr14:35502400-35503600	Strong transcription	Fetal Lung	lung
44	chr14:35502400-35503600	ZNF genes & repeats	Dnd41	blood
45	chr14:35502400-35503800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
46	chr14:35502400-35503800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr14:35502400-35504600	ZNF genes & repeats	Fetal Intestine Small	intestine
48	chr14:35502600-35503400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr14:35502600-35503400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
50	chr14:35502600-35503600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell

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