Variant report

Variant	rs17839519
Chromosome Location	chr16:31722414-31722415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:31722259-31723269	GM12878	blood:	n/a	n/a
2	POLR2A	chr16:31722072-31726986	GM12891	blood:	n/a	n/a
3	POLR2A	chr16:31721524-31724927	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:31718748-31725396	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:31721040-31725468	GM12892	blood:	n/a	n/a
6	POLR2A	chr16:31721971-31724056	K562	blood:	n/a	n/a
7	POLR2A	chr16:31721894-31723279	GM12891	blood:	n/a	n/a
8	POLR2A	chr16:31721903-31722623	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr16:31721952-31722512	GM12878	blood:	n/a	n/a
10	POLR2A	chr16:31722220-31722504	HCT-116	colon:	n/a	n/a
11	POLR2A	chr16:31722239-31722487	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr16:31722009-31722468	GM12892	blood:	n/a	n/a
13	POLR2A	chr16:31722202-31722523	HepG2	liver:	n/a	n/a
14	POLR2A	chr16:31721768-31725377	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr16:31721910-31723203	GM12891	blood:	n/a	n/a
16	POLR2A	chr16:31721480-31723978	GM12878	blood:	n/a	n/a
17	POLR2A	chr16:31722061-31722517	GM12878	blood:	n/a	n/a
18	POLR2A	chr16:31722386-31723180	GM18951	blood:	n/a	n/a
19	POLR2A	chr16:31721901-31723897	GM19193	blood:	n/a	n/a
20	POLR2A	chr16:31721427-31725398	K562	blood:	n/a	n/a
21	POLR2A	chr16:31722143-31723158	GM15510	blood:	n/a	n/a
22	POLR2A	chr16:31722404-31722571	Hela-S3	cervix:	n/a	n/a
23	MBD4	chr16:31722107-31723944	HepG2	liver:	n/a	n/a
24	MYBL2	chr16:31722263-31723707	HepG2	liver:	n/a	n/a
25	POLR2A	chr16:31721574-31723176	GM12891	blood:	n/a	n/a
26	HEY1	chr16:31722180-31723092	HepG2	liver:	n/a	n/a
27	CTCF	chr16:31722400-31722550	K562	blood:	n/a	n/a
28	POLR2A	chr16:31721196-31725172	HepG2	liver:	n/a	n/a
29	FOSL2	chr16:31722023-31723986	HepG2	liver:	n/a	chr16:31723074-31723088
30	POLR2A	chr16:31721910-31723969	HepG2	liver:	n/a	n/a
31	POLR2A	chr16:31722132-31725241	MCF-7	breast:	n/a	n/a
32	POLR2A	chr16:31718943-31727784	HepG2	liver:	n/a	n/a
33	POLR2A	chr16:31721976-31723224	GM12878	blood:	n/a	n/a
34	POLR2A	chr16:31715130-31726933	HepG2	liver:	n/a	n/a
35	POLR2A	chr16:31721628-31723834	GM12892	blood:	n/a	n/a
36	POLR2A	chr16:31721890-31723251	K562	blood:	n/a	n/a
37	POLR2A	chr16:31722278-31722441	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr16:31722077-31722585	GM12892	blood:	n/a	n/a
39	POLR2A	chr16:31718974-31728173	GM12878	blood:	n/a	n/a
40	POLR2A	chr16:31721769-31727677	HepG2	liver:	n/a	n/a
41	POLR2A	chr16:31721944-31727184	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31512832..31514586-chr16:31721396..31723098,2	MCF-7	breast:
2	chr16:31517279..31520874-chr16:31722197..31727504,6	MCF-7	breast:
3	chr16:31467317..31473648-chr16:31720179..31727010,13	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF720	TF binding region
ENSG00000260625	Chromatin interaction
ENSG00000140688	Chromatin interaction
ENSG00000140691	Chromatin interaction
ENSG00000260267	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1034614	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11859426	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11861974	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11862133	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11862739	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11864739	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11864893	0.89[EUR][1000 genomes]
rs11864895	0.86[EUR][1000 genomes]
rs11865512	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11866346	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11866699	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11866828	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17535906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17839515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17839518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17839521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17839522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17839526	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2359234	0.89[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2884666	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34146726	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3751741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3794674	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs4349165	0.82[EUR][1000 genomes]
rs4417563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56935657	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57283435	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57475804	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59413238	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60195538	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60286885	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60382362	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61548031	0.94[EUR][1000 genomes]
rs7187594	0.89[ASW][hapmap];0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7192946	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7193169	0.84[EUR][1000 genomes]
rs7194865	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7195523	0.94[EUR][1000 genomes]
rs7200637	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[YRI][hapmap];0.94[EUR][1000 genomes]
rs8046495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8054672	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8056595	0.94[EUR][1000 genomes]
rs8057733	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8062014	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
2	esv3344221	chr16:31526786-31821640	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	esv3323903	chr16:31526802-31821640	Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv3504445	chr16:31526873-31821580	Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	esv3504446	chr16:31526873-31821580	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	esv3366795	chr16:31534951-31827424	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv833195	chr16:31576112-31763222	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv1057598	chr16:31608831-31726446	Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv1067321	chr16:31652036-31959992	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv918074	chr16:31669781-31935033	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv1063037	chr16:31669981-31934894	Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv542903	chr16:31669981-31934894	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31712600-31724200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr16:31712600-31724200	Weak transcription	Psoas Muscle	Psoas
3	chr16:31712600-31724200	Weak transcription	HSMM	muscle
4	chr16:31712800-31724200	Weak transcription	HSMMtube	muscle
5	chr16:31712800-31724200	Weak transcription	NHDF-Ad	bronchial
6	chr16:31712800-31724400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr16:31712800-31724600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr16:31713000-31724400	Weak transcription	Right Atrium	heart
9	chr16:31713200-31724000	Weak transcription	Fetal Heart	heart
10	chr16:31713200-31724200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr16:31713400-31724000	Weak transcription	K562	blood
12	chr16:31713400-31724200	Weak transcription	Fetal Brain Male	brain
13	chr16:31713800-31722600	Strong transcription	Fetal Stomach	stomach
14	chr16:31714000-31722800	Strong transcription	Fetal Brain Female	brain
15	chr16:31714600-31724200	Weak transcription	Fetal Kidney	kidney
16	chr16:31715800-31724200	Weak transcription	NHLF	lung
17	chr16:31716200-31724200	Weak transcription	Hela-S3	cervix
18	chr16:31717200-31723400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr16:31718000-31724200	Weak transcription	Stomach Mucosa	stomach
20	chr16:31718200-31724200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr16:31718200-31724200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr16:31718600-31724000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr16:31718600-31724200	Weak transcription	Colon Smooth Muscle	Colon
24	chr16:31719000-31724400	Weak transcription	Osteobl	bone
25	chr16:31719200-31724600	Weak transcription	Small Intestine	intestine
26	chr16:31719400-31724000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr16:31719600-31724400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr16:31719800-31724000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr16:31719800-31724000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr16:31719800-31724000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr16:31719800-31724200	Weak transcription	Primary B cells from cord blood	blood
32	chr16:31719800-31724200	Weak transcription	Brain Angular Gyrus	brain
33	chr16:31719800-31724200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr16:31719800-31724200	Weak transcription	A549	lung
35	chr16:31720000-31723800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr16:31720000-31724000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr16:31720000-31724200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr16:31720000-31724200	Weak transcription	Adipose Nuclei	Adipose
39	chr16:31720000-31724200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr16:31720000-31724200	Weak transcription	Colonic Mucosa	Colon
41	chr16:31720000-31724200	Weak transcription	Ovary	ovary
42	chr16:31720200-31724000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr16:31720200-31724000	Weak transcription	Brain Hippocampus Middle	brain
44	chr16:31720200-31724000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr16:31720200-31724200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr16:31720200-31724200	Weak transcription	Fetal Lung	lung
47	chr16:31720400-31722800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr16:31720400-31723000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr16:31720400-31723000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr16:31720400-31723400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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