Variant report

Variant	rs62405531
Chromosome Location	chr5:179959979-179959980
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11249715	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11249724	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738060	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11740103	0.81[AMR][1000 genomes]
rs11740121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740213	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11740953	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741030	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11742350	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742375	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743486	0.81[AMR][1000 genomes]
rs11744382	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11744428	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744582	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11745477	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11745688	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11746130	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11747624	0.81[AMR][1000 genomes]
rs11748724	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11748792	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11750477	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11750835	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11949203	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950075	0.84[ASN][1000 genomes]
rs11956078	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11957507	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11960298	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12109328	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12110046	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12719870	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13154631	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13156947	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13164771	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13166694	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13171439	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13171609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171921	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13174480	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13179742	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13181735	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13182919	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13183429	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13187624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17630549	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17698422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002074	0.83[ASN][1000 genomes]
rs34281336	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35076338	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35197594	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35490561	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35706747	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56005965	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56039468	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60034484	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62405495	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62405496	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62405525	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62405532	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62405547	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs872365	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs872366	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
4	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
6	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
7	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv1023537	chr5:179791679-179982822	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv537985	chr5:179791679-179982822	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv830564	chr5:179867394-180010096	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	esv1810959	chr5:179945112-179997861	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179946200-179960800	Weak transcription	NHLF	lung
2	chr5:179950200-179975200	Weak transcription	Psoas Muscle	Psoas
3	chr5:179950200-179984400	Weak transcription	NHDF-Ad	bronchial
4	chr5:179950200-179992000	Weak transcription	Right Ventricle	heart
5	chr5:179950400-179992400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr5:179950600-180004000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:179951000-179991800	Weak transcription	Small Intestine	intestine
8	chr5:179951600-179967000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:179952400-179969000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:179952800-179967200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:179952800-179975400	Weak transcription	Stomach Mucosa	stomach
12	chr5:179953400-179975200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:179953600-179977000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr5:179953800-179975400	Weak transcription	Fetal Heart	heart
15	chr5:179954000-179962600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:179954000-179964400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:179954600-179964200	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:179955600-179962800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:179955600-179977600	Weak transcription	Colonic Mucosa	Colon
20	chr5:179956200-179960000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:179956200-179962800	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:179956200-179963800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr5:179956200-179964400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:179956200-179964800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:179956400-179962800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:179956600-179961800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr5:179956600-179962400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:179956600-179964400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:179956600-179964400	Strong transcription	Fetal Muscle Leg	muscle
30	chr5:179956800-179961800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:179956800-179964600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:179957000-179960800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:179957000-179962200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:179957000-179962400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:179957200-179960600	Weak transcription	K562	blood
36	chr5:179957200-179961600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:179957400-179964200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:179957400-179976800	Weak transcription	Osteobl	bone
39	chr5:179957600-179964200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:179957600-179965800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:179957600-179967200	Weak transcription	A549	lung
42	chr5:179957600-179967200	Weak transcription	NH-A	brain
43	chr5:179958200-179960200	Strong transcription	Spleen	Spleen
44	chr5:179958200-179962200	Strong transcription	Fetal Stomach	stomach
45	chr5:179958200-179971000	Weak transcription	HUVEC	blood vessel
46	chr5:179958400-179961400	Strong transcription	Lung	lung
47	chr5:179958400-179964200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr5:179958600-179960200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
49	chr5:179958600-179960400	Strong transcription	Gastric	stomach
50	chr5:179958600-179961400	Strong transcription	Rectal Mucosa Donor 29	rectum

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