Variant report

Variant	rs16970240
Chromosome Location	chr16:70543111-70543112
allele	C/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	CTCF	chr16:70543000-70543150	HCPEpiC	choroid plexus:	n/a	n/a
2	WRNIP1	chr16:70542928-70543276	GM12878	blood:	n/a	n/a
3	CTCF	chr16:70543000-70543150	GM12870	blood:	n/a	n/a
4	RAD21	chr16:70542629-70543132	HCT-116	colon:	n/a	chr16:70542830-70542849
5	CTCF	chr16:70543040-70543190	SAEC	small airway:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:70412934..70415272-chr16:70540814..70543390,2	MCF-7	breast:
2	chr16:70540803..70547043-chr16:70555255..70559706,8	MCF-7	breast:
3	chr16:70538068..70540802-chr16:70542880..70545267,2	MCF-7	breast:
4	chr16:70488713..70490555-chr16:70542927..70545450,2	K562	blood:
5	chr16:70542244..70550034-chr16:70550058..70558887,15	MCF-7	breast:

Variant related genes	Relation type
COG4	TF binding region
ENSG00000103051	Chromatin interaction
ENSG00000260111	Chromatin interaction
ENSG00000189091	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs13331220	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13332431	1.00[TSI][hapmap]
rs13334577	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs13339216	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13339561	1.00[AMR][1000 genomes]
rs13339593	1.00[AMR][1000 genomes]
rs13339643	1.00[AMR][1000 genomes]
rs16970226	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970243	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970253	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970259	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970260	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17878662	1.00[AMR][1000 genomes]
rs17879275	1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs17881316	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17885165	1.00[AMR][1000 genomes]
rs17886111	1.00[AMR][1000 genomes]
rs28419202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28438025	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28475204	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28619389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28777081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55667445	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55885171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55926204	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs56189591	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57451547	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58142695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58144908	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58885322	1.00[EUR][1000 genomes]
rs59158714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59460917	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60757048	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61641432	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61692284	1.00[EUR][1000 genomes]
rs6499318	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7184876	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7185011	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7185462	1.00[EUR][1000 genomes]
rs7186436	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7188297	1.00[AMR][1000 genomes]
rs7188474	1.00[AMR][1000 genomes]
rs7188808	1.00[AMR][1000 genomes]
rs7191191	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7193228	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7196773	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7199312	1.00[AMR][1000 genomes]
rs7200034	1.00[MEX][hapmap]
rs7200586	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7200978	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73573163	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73573175	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73578815	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73578819	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8047593	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8049929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8050767	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8050782	1.00[EUR][1000 genomes]
rs8051473	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8051618	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8057327	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8057732	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8057766	0.90[LWK][hapmap];1.00[MEX][hapmap]
rs8058754	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8059200	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8061243	1.00[AMR][1000 genomes]
rs8061431	1.00[AMR][1000 genomes]
rs8062414	0.93[YRI][hapmap];1.00[AMR][1000 genomes]
rs8062794	1.00[AMR][1000 genomes]
rs9302615	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9921410	1.00[AMR][1000 genomes]
rs9921696	0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs9924352	1.00[MEX][hapmap]
rs9925510	0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs9926355	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9926435	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928617	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9928808	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9929182	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9929354	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9929882	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9932065	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9932939	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933022	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9936085	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9937769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9939252	0.91[AFR][1000 genomes]
rs9940353	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	esv2830027	chr16:70473934-70558039	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70489400-70556400	Weak transcription	Stomach Mucosa	stomach
2	chr16:70512800-70556400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:70518000-70545800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:70528000-70553800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr16:70528800-70556400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr16:70530600-70545800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr16:70531400-70543600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr16:70532000-70545600	Weak transcription	A549	lung
9	chr16:70536600-70554000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr16:70536800-70546200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr16:70536800-70554000	Strong transcription	Fetal Stomach	stomach
12	chr16:70537000-70546400	Strong transcription	Fetal Intestine Small	intestine
13	chr16:70537200-70554000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr16:70537800-70552600	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr16:70537800-70553800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr16:70537800-70553800	Strong transcription	Liver	Liver
17	chr16:70538800-70552200	Strong transcription	Stomach Smooth Muscle	stomach
18	chr16:70539600-70552400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr16:70539600-70553800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr16:70539800-70543200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr16:70539800-70552000	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr16:70539800-70552600	Strong transcription	Primary T cells from cord blood	blood
23	chr16:70539800-70552600	Strong transcription	Fetal Intestine Large	intestine
24	chr16:70539800-70552600	Strong transcription	Fetal Muscle Leg	muscle
25	chr16:70539800-70553000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr16:70539800-70553800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr16:70539800-70553800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr16:70539800-70553800	Strong transcription	Placenta	Placenta
29	chr16:70540000-70546400	Strong transcription	Pancreas	Pancrea
30	chr16:70540000-70552400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr16:70540000-70553000	Strong transcription	Thymus	Thymus
32	chr16:70540200-70551000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr16:70540200-70553800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr16:70540200-70554000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr16:70540400-70544000	Strong transcription	NHLF	lung
36	chr16:70540400-70546000	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr16:70540400-70546000	Strong transcription	Osteobl	bone
38	chr16:70540400-70552600	Strong transcription	Brain Germinal Matrix	brain
39	chr16:70540600-70546200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr16:70540600-70552200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr16:70540600-70552400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr16:70540600-70552600	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr16:70540800-70551400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr16:70540800-70552200	Strong transcription	Spleen	Spleen
45	chr16:70540800-70552400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr16:70540800-70553000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr16:70541000-70544600	Strong transcription	Right Ventricle	heart
48	chr16:70541000-70546600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr16:70541000-70552400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr16:70541000-70552400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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