Variant report

Variant	rs11658116
Chromosome Location	chr17:20224290-20224291
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:277)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:277 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr17:20224170-20224366	K562	blood:	n/a	n/a
2	FOXP2	chr17:20224232-20224485	SK-N-MC	brain:	n/a	n/a
3	PAX5	chr17:20224008-20224658	GM12878	blood:	n/a	n/a
4	TCF3	chr17:20223842-20224481	GM12878	blood:	n/a	n/a
5	CTCF	chr17:20224110-20224447	HepG2	liver:	n/a	n/a
6	CTCF	chr17:20224140-20224290	HFF	foreskin:	n/a	n/a
7	JUND	chr17:20224150-20224418	HepG2	liver:	n/a	n/a
8	CTCF	chr17:20224220-20224370	GM12868	blood:	n/a	n/a
9	CTCF	chr17:20224140-20224290	BE2_C	brain:	n/a	n/a
10	RAD21	chr17:20224108-20224436	GM12878	blood:	n/a	n/a
11	CTCF	chr17:20224200-20224350	AG09309	skin:	n/a	n/a
12	EBF1	chr17:20223965-20224646	GM12878	blood:	n/a	n/a
13	CTCF	chr17:20224108-20224448	Kidney_OC	kidney:	n/a	n/a
14	BRCA1	chr17:20224258-20224346	HepG2	liver:	n/a	n/a
15	CTCF	chr17:20224140-20224290	HMEC	breast:	n/a	n/a
16	CTCF	chr17:20224200-20224350	GM12878	blood:	n/a	n/a
17	CTCF	chr17:20224140-20224290	HA-sp	spinal cord:	n/a	n/a
18	CTCF	chr17:20224200-20224350	GM12864	blood:	n/a	n/a
19	YY1	chr17:20224043-20224346	GM12892	blood:	n/a	chr17:20224179-20224188
20	CTCF	chr17:20224260-20224410	Caco-2	colon:	n/a	n/a
21	POLR2A	chr17:20224282-20224560	MCF-7	breast:	n/a	n/a
22	TEAD4	chr17:20224024-20224483	H1-hESC	embryonic stem cell:	n/a	n/a
23	BATF	chr17:20224099-20224508	GM12878	blood:	n/a	n/a
24	JUND	chr17:20224114-20224628	A549	lung:	n/a	chr17:20224410-20224419
25	CTCF	chr17:20224140-20224290	MCF-7	breast:	n/a	n/a
26	CTCF	chr17:20224117-20224402	SK-N-SH_RA	brain:	n/a	n/a
27	CTCF	chr17:20224140-20224290	GM12873	blood:	n/a	n/a
28	RAD21	chr17:20224075-20224445	HepG2	liver:	n/a	n/a
29	RAD21	chr17:20224103-20224417	SK-N-SH_RA	brain:	n/a	n/a
30	SIN3AK20	chr17:20224195-20224355	HepG2	liver:	n/a	n/a
31	JUND	chr17:20224148-20224438	H1-hESC	embryonic stem cell:	n/a	chr17:20224410-20224419
32	USF1	chr17:20224172-20224442	HepG2	liver:	n/a	n/a
33	CTCF	chr17:20224200-20224350	GM12873	blood:	n/a	n/a
34	CTCF	chr17:20224200-20224350	GM12865	blood:	n/a	n/a
35	CTCF	chr17:20224065-20224461	IMR90	lung:	n/a	n/a
36	CTCF	chr17:20224036-20224501	H1-hESC	embryonic stem cell:	n/a	n/a
37	POU2F2	chr17:20224147-20224441	GM12878	blood:	n/a	n/a
38	CTCF	chr17:20224136-20224434	LNCaP	prostate:	n/a	n/a
39	USF1	chr17:20224057-20224520	A549	lung:	n/a	n/a
40	MAZ	chr17:20223977-20224483	IMR90	lung:	n/a	n/a
41	RXRA	chr17:20224075-20224418	HepG2	liver:	n/a	n/a
42	NR3C1	chr17:20223953-20224539	A549	lung:	n/a	n/a
43	CTCF	chr17:20224096-20224452	GM13977	blood:	n/a	n/a
44	YY1	chr17:20224089-20224483	A549	lung:	n/a	chr17:20224179-20224188
45	CTCF	chr17:20224122-20224475	MCF-7	breast:	n/a	n/a
46	RAD21	chr17:20224050-20224491	IMR90	lung:	n/a	n/a
47	POU2F2	chr17:20224147-20224383	GM12878	blood:	n/a	n/a
48	SMC3	chr17:20224072-20224459	GM12878	blood:	n/a	n/a
49	CTCF	chr17:20223865-20224874	SK-N-SH	brain:	n/a	n/a
50	CTCF	chr17:20224180-20224330	NHEK	skin:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20164807..20165435-chr17:20223847..20224473,2	MCF-7	breast:

No data

Variant related genes	Relation type
CCDC144CP	TF binding region
ENSG00000266839	TF binding region

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10491107	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204300	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204423	0.83[EUR][1000 genomes]
rs11653630	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11653869	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11654942	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11657161	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11869258	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12453013	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12603372	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12938355	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12942568	0.86[EUR][1000 genomes]
rs12942627	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12949481	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12950564	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1373146	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1859407	0.82[EUR][1000 genomes]
rs1992561	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2107565	0.83[EUR][1000 genomes]
rs2158472	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2189709	0.82[EUR][1000 genomes]
rs2526459	0.81[EUR][1000 genomes]
rs2526463	0.82[EUR][1000 genomes]
rs2526465	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2526466	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2526476	0.88[EUR][1000 genomes]
rs2526477	0.88[EUR][1000 genomes]
rs2526478	0.88[EUR][1000 genomes]
rs2526481	0.87[EUR][1000 genomes]
rs2526482	0.86[EUR][1000 genomes]
rs2526486	0.83[EUR][1000 genomes]
rs2703770	0.86[EUR][1000 genomes]
rs2703771	0.88[EUR][1000 genomes]
rs2703776	0.89[EUR][1000 genomes]
rs2703777	0.89[EUR][1000 genomes]
rs2703781	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2703786	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2703788	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2703795	0.81[EUR][1000 genomes]
rs2703800	0.83[EUR][1000 genomes]
rs2703803	0.84[EUR][1000 genomes]
rs2703805	0.85[EUR][1000 genomes]
rs2703807	0.85[EUR][1000 genomes]
rs2703812	0.85[EUR][1000 genomes]
rs2703814	0.86[EUR][1000 genomes]
rs2703819	0.87[EUR][1000 genomes]
rs28696294	0.82[EUR][1000 genomes]
rs3850779	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3850780	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4925090	0.81[EUR][1000 genomes]
rs4925091	0.81[EUR][1000 genomes]
rs57837691	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62066870	0.81[EUR][1000 genomes]
rs67217337	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71372302	0.84[AMR][1000 genomes]
rs7211343	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7212571	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7219615	0.87[EUR][1000 genomes]
rs7223476	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73309111	0.90[ASN][1000 genomes]
rs733794	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs757494	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs757495	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8071274	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8080649	0.81[EUR][1000 genomes]
rs9901336	0.81[EUR][1000 genomes]
rs9901796	0.80[EUR][1000 genomes]
rs9912844	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv428669	chr17:20071969-20245033	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1064854	chr17:20086562-20225751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv2761953	chr17:20086562-20225763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
7	nsv1065758	chr17:20141912-20464366	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv543262	chr17:20141912-20464366	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv1057389	chr17:20158343-20256498	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv427993	chr17:20171398-20482061	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv916440	chr17:20171468-20839266	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
12	nsv520772	chr17:20184501-20522444	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
13	nsv521025	chr17:20198024-20514921	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
14	esv32786	chr17:20219434-20294008	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv471495	chr17:20221409-20464225	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
16	nsv1059504	chr17:20222112-20581021	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11658116	KRT16P3	cis	Esophagus Mucosa	GTEx
rs11658116	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20213000-20226600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr17:20218800-20224400	Weak transcription	Gastric	stomach
3	chr17:20219200-20224600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr17:20219400-20229200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr17:20221400-20224400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr17:20222000-20225000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr17:20223600-20224800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr17:20223800-20224600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr17:20223800-20224600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr17:20223800-20224600	Enhancers	Fetal Thymus	thymus
11	chr17:20223800-20224600	Active TSS	Rectal Smooth Muscle	rectum
12	chr17:20223800-20224800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr17:20223800-20224800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr17:20223800-20224800	Active TSS	Osteobl	bone
15	chr17:20223800-20225000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:20223800-20225000	Active TSS	Brain Cingulate Gyrus	brain
17	chr17:20223800-20225000	Enhancers	Esophagus	oesophagus
18	chr17:20224000-20224400	Enhancers	Placenta	Placenta
19	chr17:20224000-20224600	Active TSS	Brain Hippocampus Middle	brain
20	chr17:20224000-20224600	Enhancers	Brain Substantia Nigra	brain
21	chr17:20224000-20224600	ZNF genes & repeats	Fetal Intestine Large	intestine
22	chr17:20224000-20224600	Enhancers	Fetal Muscle Trunk	muscle
23	chr17:20224000-20224600	Enhancers	Spleen	Spleen
24	chr17:20224000-20224600	Enhancers	HMEC	breast
25	chr17:20224000-20224600	Enhancers	NHEK	skin
26	chr17:20224000-20224800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:20224000-20224800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:20224000-20224800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr17:20224000-20224800	Active TSS	Fetal Stomach	stomach
30	chr17:20224200-20224400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:20224200-20224400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr17:20224200-20224400	Active TSS	Right Ventricle	heart
33	chr17:20224200-20224600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr17:20224200-20224600	Enhancers	Primary B cells from peripheral blood	blood
35	chr17:20224200-20224600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr17:20224200-20224600	Enhancers	Adipose Nuclei	Adipose
37	chr17:20224200-20224600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr17:20224200-20224600	Enhancers	Ovary	ovary
39	chr17:20224200-20224600	Enhancers	Pancreas	Pancrea
40	chr17:20224200-20224600	Enhancers	Right Atrium	heart
41	chr17:20224200-20224800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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