Variant report

Variant	rs61404039
Chromosome Location	chr16:72118418-72118419
allele	A/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	chr16:72116485-72119281	K562	blood:	n/a	n/a
2	CBX3	chr16:72118288-72118762	K562	blood:	n/a	n/a
3	KAP1	chr16:72118177-72118743	K562	blood:	n/a	chr16:72118279-72118287
4	POLR2A	chr16:72118312-72118426	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr16:72118286-72118545	K562	blood:	n/a	n/a
6	TRIM28	chr16:72118303-72118748	K562	blood:	n/a	n/a
7	POLR2A	chr16:72118393-72118579	Hela-S3	cervix:	n/a	n/a
8	SETDB1	chr16:72118346-72118912	U2OS	brain:	n/a	n/a
9	SETDB1	chr16:72118341-72118923	K562	blood:	n/a	n/a
10	CBX3	chr16:72118343-72118710	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72117553..72119364-chr16:72127046..72129363,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260252	TF binding region
ENSG00000140829	Chromatin interaction
ENSG00000140830	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1065360	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11554764	0.92[ASN][1000 genomes]
rs12923749	0.81[ASN][1000 genomes]
rs12926250	0.81[ASN][1000 genomes]
rs12928056	0.81[ASN][1000 genomes]
rs12933482	0.81[ASN][1000 genomes]
rs17590101	0.92[ASN][1000 genomes]
rs17604662	0.81[ASN][1000 genomes]
rs17604676	0.81[ASN][1000 genomes]
rs17666271	0.92[ASN][1000 genomes]
rs17667639	0.81[ASN][1000 genomes]
rs17667675	0.81[ASN][1000 genomes]
rs2021171	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35448862	0.92[ASN][1000 genomes]
rs35930480	0.81[ASN][1000 genomes]
rs36012445	0.81[ASN][1000 genomes]
rs36125653	0.81[ASN][1000 genomes]
rs3815192	0.92[ASN][1000 genomes]
rs3852783	0.82[ASN][1000 genomes]
rs4788606	0.89[ASN][1000 genomes]
rs4788612	0.92[ASN][1000 genomes]
rs55772151	0.92[ASN][1000 genomes]
rs56901884	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59049640	0.85[ASN][1000 genomes]
rs59958340	0.81[ASN][1000 genomes]
rs60449783	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61060922	0.92[ASN][1000 genomes]
rs61258384	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61282680	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61733129	0.81[ASN][1000 genomes]
rs71386950	0.92[ASN][1000 genomes]
rs71386951	0.81[ASN][1000 genomes]
rs74029810	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74029814	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74029815	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74029840	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8182209	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9652628	0.81[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	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
7	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
9	nsv978167	chr16:72088322-72118671	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
10	esv1808086	chr16:72088669-72128767	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers 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	22 gene(s)	inside rSNPs	n/a
11	esv3343168	chr16:72111500-72128436	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72106600-72126400	Weak transcription	Small Intestine	intestine
2	chr16:72108000-72126400	Weak transcription	Fetal Heart	heart
3	chr16:72108400-72118600	Weak transcription	Colon Smooth Muscle	Colon
4	chr16:72108400-72119000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr16:72108800-72118600	Weak transcription	K562	blood
6	chr16:72108800-72118800	Weak transcription	Gastric	stomach
7	chr16:72109000-72118600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr16:72109000-72122600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr16:72109600-72118600	Weak transcription	Stomach Mucosa	stomach
10	chr16:72110000-72118600	Weak transcription	HSMM	muscle
11	chr16:72110200-72122800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr16:72111000-72120000	Weak transcription	NHLF	lung
13	chr16:72111200-72118600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr16:72116000-72118600	Weak transcription	Fetal Kidney	kidney
15	chr16:72116200-72118600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr16:72116800-72118600	Weak transcription	NH-A	brain
17	chr16:72116800-72119000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr16:72117000-72118600	Weak transcription	Hela-S3	cervix
19	chr16:72117000-72118600	Weak transcription	NHDF-Ad	bronchial
20	chr16:72117000-72119400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
21	chr16:72117000-72126600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr16:72117200-72118600	Weak transcription	HUVEC	blood vessel
23	chr16:72117200-72119600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr16:72117600-72118800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr16:72117800-72118800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr16:72117800-72119200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
27	chr16:72117800-72119200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr16:72117800-72119200	ZNF genes & repeats	Thymus	Thymus
29	chr16:72117800-72119200	ZNF genes & repeats	A549	lung
30	chr16:72117800-72119400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr16:72117800-72119400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
32	chr16:72117800-72119400	ZNF genes & repeats	Primary B cells from cord blood	blood
33	chr16:72117800-72119400	ZNF genes & repeats	Primary T cells from cord blood	blood
34	chr16:72117800-72119400	ZNF genes & repeats	Esophagus	oesophagus
35	chr16:72117800-72119400	ZNF genes & repeats	Fetal Stomach	stomach
36	chr16:72117800-72119600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr16:72117800-72119600	ZNF genes & repeats	Fetal Intestine Small	intestine
38	chr16:72117800-72124400	Strong transcription	Brain Angular Gyrus	brain
39	chr16:72117800-72124600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr16:72117800-72125000	Strong transcription	Brain Hippocampus Middle	brain
41	chr16:72118000-72118800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr16:72118000-72119000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr16:72118000-72119000	Strong transcription	Left Ventricle	heart
44	chr16:72118000-72119200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
45	chr16:72118000-72119200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr16:72118000-72119400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
47	chr16:72118000-72119400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
48	chr16:72118000-72119400	ZNF genes & repeats	Dnd41	blood
49	chr16:72118000-72119400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
50	chr16:72118000-72119600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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