Variant report

Variant	rs62405497
Chromosome Location	chr5:179919912-179919913
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179919818-179919960	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179720972..179723069-chr5:179918796..179921248,2	MCF-7	breast:
2	chr5:179919075..179921338-chr5:180210769..180213087,2	MCF-7	breast:

Variant related genes	Relation type
CNOT6	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10464103	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10516143	0.81[EUR][1000 genomes]
rs10516144	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10516145	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10903256	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10903257	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10903261	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1105972	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11249716	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11249717	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11249719	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11249720	0.87[ASN][1000 genomes]
rs11249722	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11249723	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11249725	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11738044	0.81[EUR][1000 genomes]
rs11740950	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11742093	0.87[ASN][1000 genomes]
rs11743298	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11748611	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11748880	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11750412	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11750506	0.81[EUR][1000 genomes]
rs11949971	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11956294	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12187407	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12188182	0.81[EUR][1000 genomes]
rs13154251	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13164926	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13168976	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13169807	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13171802	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13172721	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13174261	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13175241	0.92[ASN][1000 genomes]
rs13181218	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13182715	0.89[ASN][1000 genomes]
rs13185444	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13361838	0.86[ASN][1000 genomes]
rs2131811	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2387284	0.81[EUR][1000 genomes]
rs2387287	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2387288	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2617262	0.89[ASN][1000 genomes]
rs34294053	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4002641	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62405523	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62405524	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62405545	0.89[ASN][1000 genomes]
rs67607816	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6859296	0.81[EUR][1000 genomes]
rs6879011	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6887532	0.97[ASN][1000 genomes]
rs6888064	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6897365	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7705421	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7722020	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7726226	0.90[ASN][1000 genomes]
rs7727679	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs937919	0.92[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	nsv1019519	chr5:179866730-179959408	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	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

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179900000-179920400	Weak transcription	A549	lung
2	chr5:179911800-179920200	Weak transcription	Pancreas	Pancrea
3	chr5:179912000-179920400	Weak transcription	NHDF-Ad	bronchial
4	chr5:179914200-179920400	Weak transcription	Fetal Stomach	stomach
5	chr5:179914600-179920400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr5:179915000-179921000	Weak transcription	Aorta	Aorta
7	chr5:179915600-179920400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:179916400-179920400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:179916800-179920400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:179917400-179920800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:179917800-179920400	Weak transcription	Brain Angular Gyrus	brain
12	chr5:179918200-179920400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:179918400-179921000	Weak transcription	Lung	lung
14	chr5:179918600-179920000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr5:179918600-179920400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:179918600-179920400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:179918600-179921000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:179918600-179921000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:179918800-179920000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:179918800-179920400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:179918800-179921600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:179919000-179920200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:179919000-179920400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:179919000-179920400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr5:179919000-179920600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:179919000-179920800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr5:179919000-179921000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr5:179919000-179921000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr5:179919200-179920400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr5:179919400-179920000	Enhancers	Dnd41	blood
31	chr5:179919400-179920400	Enhancers	Brain Anterior Caudate	brain
32	chr5:179919400-179920600	Enhancers	Placenta	Placenta
33	chr5:179919400-179920800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr5:179919600-179920200	Enhancers	K562	blood
35	chr5:179919600-179920600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr5:179919800-179920200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr5:179919800-179920400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr5:179919800-179920400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:179919800-179920600	Enhancers	HepG2	liver
40	chr5:179919800-179920800	Enhancers	Fetal Thymus	thymus
41	chr5:179919800-179921400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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