Variant report

Variant	rs9323443
Chromosome Location	chr14:64409015-64409016
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	chr14:64407990..64410133-chr14:64411071..64414129,3	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10149728	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[EUR][1000 genomes]
rs10498512	0.88[EUR][1000 genomes]
rs10873172	0.80[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[MEX][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11621026	0.84[MEX][hapmap]
rs11623650	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1255856	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1255857	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1255867	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1255869	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255872	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1255873	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1255874	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1255875	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1255876	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1255877	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255878	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1255879	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1255880	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1255881	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1255882	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1255883	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1255885	0.93[EUR][1000 genomes]
rs1255887	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1255890	0.91[EUR][1000 genomes]
rs1255891	0.91[EUR][1000 genomes]
rs1255892	0.91[EUR][1000 genomes]
rs1255896	0.89[EUR][1000 genomes]
rs1255900	0.88[EUR][1000 genomes]
rs1255901	0.88[EUR][1000 genomes]
rs1255902	0.88[EUR][1000 genomes]
rs1255903	0.86[EUR][1000 genomes]
rs1255905	0.88[EUR][1000 genomes]
rs1255908	0.89[EUR][1000 genomes]
rs1262235	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1262237	0.91[EUR][1000 genomes]
rs1266870	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1270051	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1270526	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1271567	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs1272156	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[EUR][1000 genomes]
rs1272714	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1273192	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12878653	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12881652	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2184292	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2357175	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2357176	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2792201	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28483877	0.88[EUR][1000 genomes]
rs2884111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2994421	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2994422	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35224808	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61984073	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7156570	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009321	0.88[EUR][1000 genomes]
rs9323442	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs945027	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs945028	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1038825	chr14:64109441-64491720	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037140	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv542119	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv564904	chr14:64346190-64416898	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1793389	chr14:64346190-64457224	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9323443	KCNH5	cis	parietal	SCAN
rs9323443	C14orf39	cis	cerebellum	SCAN
rs9323443	SYNE2	cis	cerebellum	SCAN
rs9323443	DAAM1	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64365000-64430200	Weak transcription	Fetal Brain Male	brain
2	chr14:64376000-64416200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr14:64378000-64416200	Weak transcription	Fetal Lung	lung
4	chr14:64378400-64416000	Weak transcription	Primary B cells from cord blood	blood
5	chr14:64387000-64416400	Weak transcription	Aorta	Aorta
6	chr14:64390200-64416400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr14:64390600-64418800	Weak transcription	HepG2	liver
8	chr14:64393200-64419800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr14:64393800-64414800	Weak transcription	Fetal Muscle Leg	muscle
10	chr14:64395000-64491000	Weak transcription	Psoas Muscle	Psoas
11	chr14:64396000-64418600	Weak transcription	Fetal Heart	heart
12	chr14:64400000-64416400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr14:64400000-64419800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr14:64400400-64409600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr14:64400800-64417800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr14:64401000-64416200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr14:64401000-64416400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr14:64401400-64430200	Weak transcription	Stomach Mucosa	stomach
19	chr14:64401600-64416600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr14:64401600-64427800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr14:64403600-64432800	Weak transcription	Lung	lung
22	chr14:64404200-64416200	Weak transcription	Right Ventricle	heart
23	chr14:64404200-64416600	Weak transcription	Adipose Nuclei	Adipose
24	chr14:64405000-64423400	Weak transcription	HSMM	muscle
25	chr14:64405400-64409600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr14:64405600-64416200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr14:64405600-64416200	Weak transcription	NHEK	skin
28	chr14:64405600-64418800	Weak transcription	HMEC	breast
29	chr14:64405800-64409200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr14:64405800-64416200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr14:64405800-64418800	Weak transcription	Small Intestine	intestine
32	chr14:64406000-64416200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr14:64406000-64416600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr14:64406000-64416600	Weak transcription	Gastric	stomach
35	chr14:64406000-64416600	Weak transcription	Pancreas	Pancrea
36	chr14:64406000-64416600	Weak transcription	Spleen	Spleen
37	chr14:64406200-64434400	Weak transcription	Hela-S3	cervix
38	chr14:64406800-64410000	Strong transcription	Left Ventricle	heart
39	chr14:64407000-64409200	Strong transcription	Fetal Brain Female	brain
40	chr14:64407200-64410000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr14:64407200-64410000	Strong transcription	Liver	Liver
42	chr14:64407200-64410400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr14:64407200-64416000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr14:64407200-64418800	Weak transcription	HUVEC	blood vessel
45	chr14:64407400-64410200	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr14:64407600-64409200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr14:64407600-64410000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr14:64407600-64410200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr14:64407600-64410200	Strong transcription	Dnd41	blood
50	chr14:64407800-64410000	Strong transcription	HUES64 Cell Line	embryonic stem cell

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