Variant report

Variant	rs12920529
Chromosome Location	chr16:70679488-70679489
allele	G/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	RAD21	chr16:70679128-70679508	H1-hESC	embryonic stem cell:	n/a	chr16:70679332-70679342
2	CTCF	chr16:70679066-70679606	K562	blood:	n/a	chr16:70679112-70679125 chr16:70679329-70679338
3	CTCF	chr16:70679183-70679490	K562	blood:	n/a	chr16:70679329-70679338
4	RAD21	chr16:70679033-70679608	HCT-116	colon:	n/a	chr16:70679109-70679123 chr16:70679113-70679126 chr16:70679332-70679342
5	ZNF263	chr16:70678499-70679564	HEK293-T-REx	kidney:	n/a	chr16:70679345-70679354 chr16:70678829-70678850 chr16:70678797-70678818
6	CTCF	chr16:70679181-70679500	HepG2	liver:	n/a	chr16:70679329-70679338
7	RAD21	chr16:70679109-70679526	H1-hESC	embryonic stem cell:	n/a	chr16:70679109-70679123 chr16:70679113-70679126 chr16:70679332-70679342
8	RAD21	chr16:70679055-70679555	HCT-116	colon:	n/a	chr16:70679109-70679123 chr16:70679113-70679126 chr16:70679332-70679342
9	RAD21	chr16:70679081-70679565	ECC-1	luminal epithelium:	n/a	chr16:70679109-70679123 chr16:70679113-70679126 chr16:70679332-70679342
10	RAD21	chr16:70679140-70679584	MCF-7	breast:	n/a	chr16:70679332-70679342

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:70677228..70680098-chr16:70680476..70682009,2	K562	blood:
2	chr16:70556330..70559172-chr16:70679219..70681139,2	MCF-7	breast:

Variant related genes	Relation type
IL34	TF binding region
ENSG00000103051	Chromatin interaction
ENSG00000189091	Chromatin interaction
ENSG00000157368	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11865804	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11866403	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12596070	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12596475	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12598248	0.82[EUR][1000 genomes]
rs12598251	0.82[EUR][1000 genomes]
rs12598456	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12598945	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12598955	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12919296	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12919451	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12920334	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12923477	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12923630	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12923637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12924304	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12925493	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12926402	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12929463	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12929508	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12935541	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13329733	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1551530	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16970408	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1973089	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1973090	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs33998678	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34426756	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34644948	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34692833	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34811595	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34881169	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35283920	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35285555	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35290416	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35381200	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35437297	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35794088	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36097154	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3813905	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985413	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4985414	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4985415	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985546	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4985549	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4985550	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4985551	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4985552	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4985553	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55872380	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56220651	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs57738457	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57752020	0.88[AMR][1000 genomes]
rs59865481	0.88[AMR][1000 genomes]
rs61170208	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68049363	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71401818	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7191249	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7192723	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7198170	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8060584	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8061329	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9933834	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517391	chr16:70666410-70840490	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv457517	chr16:70666722-70840490	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv572945	chr16:70666722-70840490	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv906874	chr16:70677785-70740707	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv906875	chr16:70677785-70742536	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv906876	chr16:70677785-70757555	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv906877	chr16:70677785-70766378	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv906878	chr16:70677785-70782922	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS 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	19 gene(s)	inside rSNPs	diseases
9	nsv906879	chr16:70677785-70790831	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv906880	chr16:70677785-70796515	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70669600-70687800	Weak transcription	Right Atrium	heart
2	chr16:70670600-70680000	Weak transcription	Fetal Intestine Small	intestine
3	chr16:70673600-70680200	Weak transcription	Brain Anterior Caudate	brain
4	chr16:70673600-70680200	Weak transcription	HSMMtube	muscle
5	chr16:70673600-70683200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr16:70673600-70684000	Weak transcription	Esophagus	oesophagus
7	chr16:70673800-70680200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr16:70673800-70680200	Weak transcription	Fetal Stomach	stomach
9	chr16:70673800-70682800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr16:70674000-70680200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr16:70674000-70680200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr16:70674200-70680200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr16:70674200-70680600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr16:70678000-70681200	Weak transcription	Fetal Intestine Large	intestine
15	chr16:70678800-70679600	Bivalent Enhancer	Fetal Brain Male	brain
16	chr16:70679000-70679600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr16:70679000-70679600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr16:70679000-70680200	Enhancers	Spleen	Spleen
19	chr16:70679000-70680600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr16:70679400-70679600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr16:70679400-70680000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr16:70679400-70680000	Enhancers	Skeletal Muscle Male	skeletal muscle

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