Variant report

Variant	rs62405496
Chromosome Location	chr5:179919618-179919619
allele	C/T
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	ZNF263	chr5:179919447-179919780	HEK293-T-REx	kidney:	n/a	n/a
2	POLR2A	chr5:179919521-179919682	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:179919474-179919665	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: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11249715	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11249724	0.84[ASN][1000 genomes]
rs11740103	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11740121	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11740213	0.81[AMR][1000 genomes]
rs11740953	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11741030	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11742350	0.84[ASN][1000 genomes]
rs11742375	0.84[ASN][1000 genomes]
rs11743486	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11744382	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11744428	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11744582	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11745477	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11745688	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11747624	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11748724	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11750477	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11949203	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11956078	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11957507	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11960298	0.84[ASN][1000 genomes]
rs12109328	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12719870	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13154631	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13156947	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13158465	0.82[ASN][1000 genomes]
rs13162858	0.80[ASN][1000 genomes]
rs13164771	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13166694	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13171609	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13171921	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13174480	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13179742	0.81[AMR][1000 genomes]
rs13187624	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17630549	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17698422	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2002074	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34281336	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34957777	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35076338	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35197594	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35490561	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35706747	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56005965	0.81[EUR][1000 genomes]
rs56039468	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60034484	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62405490	0.82[ASN][1000 genomes]
rs62405491	0.85[ASN][1000 genomes]
rs62405495	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62405525	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62405531	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62405532	0.81[AMR][1000 genomes]
rs872365	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs872366	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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:39 , 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	chr5:179918000-179919800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:179918000-179919800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:179918200-179920400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:179918400-179921000	Weak transcription	Lung	lung
16	chr5:179918600-179920000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr5:179918600-179920400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:179918600-179920400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:179918600-179921000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:179918600-179921000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:179918800-179920000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:179918800-179920400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr5:179918800-179921600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr5:179919000-179920200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:179919000-179920400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:179919000-179920400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr5:179919000-179920600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:179919000-179920800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:179919000-179921000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr5:179919000-179921000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:179919200-179919800	Weak transcription	Fetal Thymus	thymus
32	chr5:179919200-179920400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr5:179919400-179920000	Enhancers	Dnd41	blood
34	chr5:179919400-179920400	Enhancers	Brain Anterior Caudate	brain
35	chr5:179919400-179920600	Enhancers	Placenta	Placenta
36	chr5:179919400-179920800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr5:179919600-179919800	Enhancers	Fetal Muscle Trunk	muscle
38	chr5:179919600-179920200	Enhancers	K562	blood
39	chr5:179919600-179920600	Weak transcription	H9 Cell Line	embryonic stem cell

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