Variant report

Variant	rs10165220
Chromosome Location	chr2:95537000-95537001
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	chr2:95536957-95537339	ECC-1	luminal epithelium:	n/a	n/a
2	FOXA2	chr2:95536945-95537497	A549	lung:	n/a	n/a
3	POLR2A	chr2:95536999-95537046	K562	blood:	n/a	n/a
4	CTCF	chr2:95535899-95537070	A549	lung:	n/a	chr2:95536608-95536615 chr2:95536268-95536286 chr2:95536435-95536448
5	FOXA2	chr2:95536979-95537466	A549	lung:	n/a	n/a

Variant related genes	Relation type
TEKT4	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10172167	0.86[CHB][hapmap]
rs10174668	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10178186	0.83[YRI][hapmap]
rs10180591	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10874467	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11164111	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11164112	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11883879	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12612789	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13414018	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2004626	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2077443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28680439	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34087291	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4555374	0.86[CHB][hapmap]
rs4564804	0.81[CHB][hapmap]
rs4854231	0.87[EUR][1000 genomes]
rs4854232	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4854233	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4854234	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4854235	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62146933	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62146942	0.88[ASN][1000 genomes]
rs6708474	0.87[CHB][hapmap]
rs9324212	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000661	chr2:95327875-95739468	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv2759075	chr2:95358799-95620108	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10165220	CYP4F32P	cis	Esophagus Mucosa	GTEx
rs10165220	AC073464.7	cis	Esophagus Mucosa	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95528200-95537400	Weak transcription	Gastric	stomach
2	chr2:95534200-95549400	Weak transcription	Right Atrium	heart
3	chr2:95535800-95537200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
4	chr2:95536200-95538200	ZNF genes & repeats	Lung	lung
5	chr2:95536400-95537000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:95536400-95537200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
7	chr2:95536400-95537400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr2:95536400-95537400	Bivalent Enhancer	Adipose Nuclei	Adipose
9	chr2:95536400-95537600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr2:95536400-95537600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr2:95536400-95537800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr2:95536600-95537000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
13	chr2:95536600-95537200	Weak transcription	Pancreas	Pancrea
14	chr2:95536600-95537600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr2:95536600-95537800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr2:95536600-95537800	Bivalent Enhancer	Fetal Lung	lung
17	chr2:95536600-95538000	Bivalent Enhancer	Placenta	Placenta
18	chr2:95536800-95537000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:95536800-95537000	Bivalent Enhancer	A549	lung
20	chr2:95536800-95537200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:95536800-95537600	Bivalent Enhancer	Stomach Mucosa	stomach
22	chr2:95536800-95537600	Active TSS	HSMM	muscle
23	chr2:95536800-95537800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
24	chr2:95536800-95537800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:95536800-95537800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:95537000-95537200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:95537000-95537200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:95537000-95537200	Bivalent/Poised TSS	Esophagus	oesophagus
29	chr2:95537000-95537200	Flanking Bivalent TSS/Enh	A549	lung
30	chr2:95537000-95537400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:95537000-95537400	Bivalent Enhancer	Brain Germinal Matrix	brain
32	chr2:95537000-95537400	Active TSS	Fetal Kidney	kidney
33	chr2:95537000-95537400	Bivalent Enhancer	Fetal Muscle Leg	muscle
34	chr2:95537000-95537600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr2:95537000-95537600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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