Variant report

Variant	rs66616635
Chromosome Location	chr16:79806081-79806082
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	BHLHE40	chr16:79805738-79806219	K562	blood:	n/a	n/a
2	RFX5	chr16:79803164-79806271	SK-N-SH	brain:	n/a	chr16:79804613-79804622 chr16:79804610-79804625 chr16:79804611-79804625

Variant related genes	Relation type
ENSG00000261390	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11860057	0.88[ASN][1000 genomes]
rs12448881	0.85[ASN][1000 genomes]
rs13334268	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16951260	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16951261	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16951264	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16951284	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16951299	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16951301	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16951302	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16951303	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16951310	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16951318	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16951320	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16951359	0.80[ASN][1000 genomes]
rs28420623	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28433357	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28536718	0.80[ASN][1000 genomes]
rs28691811	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4243180	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4257219	0.86[EUR][1000 genomes]
rs4302049	0.80[ASN][1000 genomes]
rs4316769	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4322684	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4327063	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4411509	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4474702	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4528586	0.80[ASN][1000 genomes]
rs4567731	0.84[ASN][1000 genomes]
rs4632145	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4889026	0.80[ASN][1000 genomes]
rs56986701	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59100419	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6564696	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6564699	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6564700	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6564701	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7188433	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7190298	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7191995	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7200600	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7202532	0.96[ASN][1000 genomes]
rs72810418	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72810426	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72810440	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73572226	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7499783	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8045678	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8056805	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8057344	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8060038	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8061610	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9673947	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9921624	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9923844	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9926635	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833296	chr16:79692236-79889727	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv833297	chr16:79732501-79920419	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv2755409	chr16:79776699-79816299	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs66616635	RP11-345M22.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79805000-79806200	Enhancers	Fetal Stomach	stomach
2	chr16:79805000-79806400	Enhancers	Fetal Lung	lung
3	chr16:79805000-79806600	Enhancers	Fetal Muscle Leg	muscle
4	chr16:79805000-79807400	Enhancers	Fetal Intestine Small	intestine
5	chr16:79805000-79807800	Enhancers	Fetal Intestine Large	intestine
6	chr16:79805000-79808800	Weak transcription	Esophagus	oesophagus
7	chr16:79805000-79809200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr16:79805000-79809400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr16:79805000-79810400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr16:79805200-79806200	Enhancers	Fetal Heart	heart
11	chr16:79805200-79806800	Enhancers	Colon Smooth Muscle	Colon
12	chr16:79805200-79806800	Enhancers	Duodenum Mucosa	Duodenum
13	chr16:79805200-79807000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr16:79805200-79807000	Enhancers	Small Intestine	intestine
15	chr16:79805200-79808600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr16:79805200-79809000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr16:79805200-79809000	Weak transcription	NHEK	skin
18	chr16:79805200-79809200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr16:79805200-79809200	Weak transcription	HMEC	breast
20	chr16:79805200-79810000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr16:79805200-79810200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr16:79805200-79810200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr16:79805200-79810200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr16:79805200-79810200	Weak transcription	Brain Hippocampus Middle	brain
25	chr16:79805200-79810200	Weak transcription	NH-A	brain
26	chr16:79805400-79809400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr16:79805400-79810200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr16:79805400-79810200	Weak transcription	Adipose Nuclei	Adipose
29	chr16:79805400-79810200	Weak transcription	Thymus	Thymus
30	chr16:79805400-79810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr16:79805400-79810400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr16:79805600-79806200	Enhancers	K562	blood
33	chr16:79805600-79810400	Weak transcription	Colonic Mucosa	Colon
34	chr16:79805800-79806200	Enhancers	Fetal Kidney	kidney
35	chr16:79805800-79806600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr16:79805800-79807200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr16:79806000-79810200	Weak transcription	Fetal Thymus	thymus
38	chr16:79806000-79810400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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