Variant report

Variant	rs10517
Chromosome Location	chr16:69743760-69743761
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:73)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:73 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr16:69743316-69743925	A549	lung:	n/a	n/a
2	RAD21	chr16:69743365-69743782	IMR90	lung:	n/a	n/a
3	POLR2A	chr16:69740530-69743833	MCF-7	breast:	n/a	n/a
4	POLR2A	chr16:69742737-69743778	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:69741274-69743842	HepG2	liver:	n/a	n/a
6	SIN3AK20	chr16:69743308-69743850	MCF-7	breast:	n/a	n/a
7	CTCF	chr16:69743373-69743825	K562	blood:	n/a	n/a
8	RAD21	chr16:69743307-69743866	ECC-1	luminal epithelium:	n/a	n/a
9	RAD21	chr16:69743430-69743791	GM12878	blood:	n/a	n/a
10	SIN3AK20	chr16:69743360-69743813	A549	lung:	n/a	n/a
11	POLR2A	chr16:69743071-69743812	Hela-S3	cervix:	n/a	n/a
12	RAD21	chr16:69743231-69743971	HCT-116	colon:	n/a	chr16:69743262-69743269
13	FOXA1	chr16:69743372-69743771	HepG2	liver:	n/a	n/a
14	RAD21	chr16:69743358-69743800	Hela-S3	cervix:	n/a	n/a
15	RAD21	chr16:69743305-69743789	MCF-7	breast:	n/a	n/a
16	CTCF	chr16:69743397-69743775	SK-N-SH_RA	brain:	n/a	n/a
17	SMC3	chr16:69743380-69743801	K562	blood:	n/a	n/a
18	RAD21	chr16:69743368-69743801	GM12878	blood:	n/a	n/a
19	RAD21	chr16:69743386-69743811	A549	lung:	n/a	n/a
20	CTCF	chr16:69743469-69743772	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr16:69743449-69743776	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr16:69739930-69743902	HepG2	liver:	n/a	n/a
23	MYC	chr16:69743447-69743777	K562	blood:	n/a	n/a
24	POLR2A	chr16:69742297-69743817	HCT-116	colon:	n/a	n/a
25	ARID3A	chr16:69743412-69743789	K562	blood:	n/a	n/a
26	CTCF	chr16:69743007-69744071	A549	lung:	n/a	n/a
27	POLR2A	chr16:69739832-69743980	A549	lung:	n/a	n/a
28	RAD21	chr16:69743336-69743765	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr16:69743231-69743905	A549	lung:	n/a	chr16:69743262-69743269
30	RAD21	chr16:69743246-69743998	HCT-116	colon:	n/a	chr16:69743262-69743269
31	ARID3A	chr16:69743402-69743803	HepG2	liver:	n/a	n/a
32	SIX5	chr16:69742984-69743901	A549	lung:	n/a	n/a
33	RAD21	chr16:69743402-69743774	SK-N-SH_RA	brain:	n/a	n/a
34	IRF1	chr16:69743484-69743771	K562	blood:	n/a	n/a
35	RFX5	chr16:69743437-69743788	K562	blood:	n/a	n/a
36	RAD21	chr16:69743367-69743805	HepG2	liver:	n/a	n/a
37	RAD21	chr16:69743362-69743764	HepG2	liver:	n/a	n/a
38	POLR2A	chr16:69743310-69743869	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr16:69743342-69743766	HepG2	liver:	n/a	n/a
40	SMC3	chr16:69743380-69743812	GM12878	blood:	n/a	n/a
41	CTCF	chr16:69743760-69743910	HEK293	kidney:	n/a	n/a
42	SMC3	chr16:69743361-69743799	HepG2	liver:	n/a	n/a
43	RAD21	chr16:69743255-69743890	MCF-7	breast:	n/a	chr16:69743262-69743269
44	POLR2A	chr16:69743345-69743829	U87	brain:	n/a	n/a
45	POLR2A	chr16:69743020-69743788	PANC-1	pancreas:	n/a	n/a
46	SIN3AK20	chr16:69743427-69743816	A549	lung:	n/a	n/a
47	POLR2A	chr16:69742991-69743866	HUVEC	blood vessel:	n/a	n/a
48	CTCF	chr16:69743321-69743807	GM12878	blood:	n/a	n/a
49	CTCF	chr16:69743364-69743873	MCF-7	breast:	n/a	n/a
50	RAD21	chr16:69743269-69743948	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:69741680..69751385-chr16:69755023..69763559,18	MCF-7	breast:
2	chr16:69741307..69747044-chr16:69787229..69790189,11	MCF-7	breast:
3	chr16:69743311..69743857-chr16:69788419..69789175,2	Hela-S3	cervix:
4	chr16:69743184..69743994-chr16:69788522..69789278,3	MCF-7	breast:
5	chr16:69743117..69744048-chr16:69788450..69789387,7	K562	blood:
6	chr16:69743463..69744034-chr16:69788837..69789372,2	MCF-7	breast:
7	chr16:69743672..69747154-chr16:69795617..69797836,3	MCF-7	breast:
8	chr16:69742300..69746801-chr16:69786779..69790470,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000238683	TF binding region
ENSG00000261602	TF binding region
ENSG00000141101	Chromatin interaction
ENSG00000198373	Chromatin interaction
ENSG00000262136	Chromatin interaction
ENSG00000181019	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10852459	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs11075736	0.86[EUR][1000 genomes]
rs1112183	0.83[JPT][hapmap]
rs1142105	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12102305	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12921017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329844	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[ASN][1000 genomes]
rs13331055	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13331071	0.85[ASN][1000 genomes]
rs13331216	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13335149	0.88[ASN][1000 genomes]
rs13335664	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13338560	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs16958965	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16958997	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16959059	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291960	0.86[TSI][hapmap]
rs2304526	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28392989	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28473508	0.82[ASN][1000 genomes]
rs2917665	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2917667	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2917669	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2917672	0.90[ASN][1000 genomes]
rs2917673	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2917674	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2917675	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2917676	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2917681	0.83[YRI][hapmap]
rs2917682	0.84[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2917683	0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2937125	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs2937126	0.80[CHD][hapmap];0.93[TSI][hapmap]
rs2937127	0.80[CHD][hapmap]
rs2965752	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2965753	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs2965757	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs2965758	0.81[CHB][hapmap]
rs3785075	0.81[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3790088	0.86[TSI][hapmap]
rs3826153	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap]
rs3826154	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3926183	0.82[ASN][1000 genomes]
rs4247109	0.82[ASW][hapmap];0.81[CHD][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs4442796	0.84[CHD][hapmap];0.83[GIH][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap]
rs4985527	0.82[ASW][hapmap];0.84[CHD][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs4985547	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs61628167	0.85[ASN][1000 genomes]
rs6499246	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6499249	0.86[CHD][hapmap];0.83[GIH][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap]
rs6499259	0.84[TSI][hapmap]
rs689452	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689456	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7184995	0.83[JPT][hapmap]
rs7200270	0.81[ASN][1000 genomes]
rs7200420	0.94[ASN][1000 genomes]
rs7204615	0.83[EUR][1000 genomes]
rs7359387	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs8057938	0.86[EUR][1000 genomes]
rs9888981	0.80[CHB][hapmap]
rs9888993	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9889219	0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs9921652	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9924264	0.86[ASN][1000 genomes]
rs9924271	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs9924953	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9925037	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.83[YRI][hapmap]
rs9927809	0.92[ASN][1000 genomes]
rs9934264	0.88[ASN][1000 genomes]
rs9934321	0.92[ASN][1000 genomes]
rs9934681	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9936464	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs9937018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9938717	0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][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	nsv906822	chr16:69711533-69745145	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	54 gene(s)	inside rSNPs	diseases
3	esv3396845	chr16:69721905-69770627	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10517	GFOD2	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69709400-69755400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr16:69726000-69755800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:69726600-69759800	Weak transcription	Psoas Muscle	Psoas
4	chr16:69726800-69747600	Weak transcription	Fetal Heart	heart
5	chr16:69728200-69746200	Weak transcription	Stomach Mucosa	stomach
6	chr16:69728200-69758600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr16:69728400-69744200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr16:69728400-69748800	Weak transcription	Gastric	stomach
9	chr16:69728400-69759200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:69728600-69752000	Weak transcription	Fetal Brain Male	brain
11	chr16:69729200-69745000	Weak transcription	Spleen	Spleen
12	chr16:69729400-69744800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr16:69729400-69745000	Weak transcription	Pancreas	Pancrea
14	chr16:69729400-69760000	Weak transcription	Brain Germinal Matrix	brain
15	chr16:69729400-69760000	Weak transcription	Ovary	ovary
16	chr16:69729600-69745000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr16:69729800-69746200	Weak transcription	Aorta	Aorta
18	chr16:69729800-69746200	Weak transcription	Left Ventricle	heart
19	chr16:69729800-69748800	Weak transcription	Esophagus	oesophagus
20	chr16:69730000-69745200	Weak transcription	Thymus	Thymus
21	chr16:69730000-69745800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr16:69730000-69759000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr16:69730200-69746000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr16:69730400-69744800	Weak transcription	Colonic Mucosa	Colon
25	chr16:69730400-69747000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr16:69730600-69759800	Weak transcription	Fetal Brain Female	brain
27	chr16:69730800-69744600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr16:69730800-69759800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr16:69731000-69746000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr16:69731800-69744400	Weak transcription	K562	blood
31	chr16:69731800-69745000	Weak transcription	Hela-S3	cervix
32	chr16:69731800-69746200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr16:69731800-69759600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr16:69731800-69759800	Weak transcription	Primary B cells from cord blood	blood
35	chr16:69731800-69759800	Weak transcription	Right Ventricle	heart
36	chr16:69732000-69746200	Weak transcription	Brain Substantia Nigra	brain
37	chr16:69732600-69744800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr16:69732600-69745000	Weak transcription	Fetal Thymus	thymus
39	chr16:69733000-69744800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr16:69733200-69745800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr16:69733400-69744800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr16:69733800-69759800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr16:69734800-69746200	Weak transcription	Fetal Intestine Large	intestine
44	chr16:69736000-69744600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr16:69736000-69744800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr16:69736000-69758600	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr16:69736600-69744400	Weak transcription	Adipose Nuclei	Adipose
48	chr16:69736600-69744400	Weak transcription	Brain Anterior Caudate	brain
49	chr16:69737000-69745400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr16:69737200-69758800	Weak transcription	Monocytes-CD14+_RO01746	blood

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