Variant report

Variant	rs16979130
Chromosome Location	chr19:44981516-44981517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:80)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:80 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF3	chr19:44980550-44981751	A549	lung:	n/a	n/a
2	TEAD4	chr19:44980700-44981679	K562	blood:	n/a	n/a
3	ELF1	chr19:44980554-44981689	A549	lung:	n/a	n/a
4	ZNF143	chr19:44981356-44981652	GM12878	blood:	n/a	n/a
5	SP1	chr19:44980615-44981763	A549	lung:	n/a	n/a
6	USF1	chr19:44981284-44981703	A549	lung:	n/a	n/a
7	ZNF274	chr19:44980580-44981772	Hela-S3	cervix:	n/a	n/a
8	USF1	chr19:44980677-44981660	A549	lung:	n/a	n/a
9	TRIM28	chr19:44981299-44981740	K562	blood:	n/a	n/a
10	RCOR1	chr19:44980215-44981892	IMR90	lung:	n/a	n/a
11	TCF12	chr19:44980414-44981825	A549	lung:	n/a	n/a
12	POLR2A	chr19:44980613-44981614	GM12892	blood:	n/a	n/a
13	POLR2A	chr19:44981391-44981637	Hela-S3	cervix:	n/a	n/a
14	ETS1	chr19:44981359-44981667	K562	blood:	n/a	n/a
15	ZBTB33	chr19:44980582-44981677	A549	lung:	n/a	n/a
16	KAP1	chr19:44980120-44982096	HEK293	kidney:	n/a	n/a
17	SETDB1	chr19:44978505-44985135	K562	blood:	n/a	n/a
18	ZBTB33	chr19:44980620-44981596	A549	lung:	n/a	n/a
19	POLR2A	chr19:44980574-44981871	HL-60	blood:	n/a	n/a
20	USF1	chr19:44980646-44981721	ECC-1	luminal epithelium:	n/a	n/a
21	KAP1	chr19:44979715-44982298	K562	blood:	n/a	n/a
22	ZNF274	chr19:44980077-44982157	HepG2	liver:	n/a	n/a
23	TCF12	chr19:44980599-44981866	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr19:44978768-44981780	K562	blood:	n/a	n/a
25	TCF12	chr19:44981339-44981653	H1-hESC	embryonic stem cell:	n/a	n/a
26	ZNF143	chr19:44980575-44981732	H1-hESC	embryonic stem cell:	n/a	n/a
27	CBX3	chr19:44980756-44981745	HCT-116	colon:	n/a	n/a
28	GATA3	chr19:44980650-44981810	A549	lung:	n/a	n/a
29	SETDB1	chr19:44978818-44983161	U2OS	brain:	n/a	n/a
30	ETS1	chr19:44980687-44981697	K562	blood:	n/a	n/a
31	POLR2A	chr19:44981306-44981628	K562	blood:	n/a	n/a
32	GTF2F1	chr19:44980686-44981730	H1-hESC	embryonic stem cell:	n/a	n/a
33	IRF1	chr19:44981354-44981660	K562	blood:	n/a	n/a
34	TCF12	chr19:44979878-44982187	A549	lung:	n/a	n/a
35	TCF12	chr19:44981356-44981670	GM12878	blood:	n/a	n/a
36	USF1	chr19:44981472-44981662	GM12878	blood:	n/a	n/a
37	USF1	chr19:44981367-44981681	H1-hESC	embryonic stem cell:	n/a	n/a
38	ATF3	chr19:44980461-44981688	A549	lung:	n/a	n/a
39	TRIM28	chr19:44980501-44981878	K562	blood:	n/a	n/a
40	POLR2A	chr19:44981376-44981719	HL-60	blood:	n/a	n/a
41	POLR2A	chr19:44980582-44981594	SK-N-MC	brain:	n/a	n/a
42	TCF12	chr19:44980557-44981822	SK-N-SH	brain:	n/a	n/a
43	SETDB1	chr19:44980597-44981861	K562	blood:	n/a	n/a
44	ZNF143	chr19:44980559-44981727	K562	blood:	n/a	n/a
45	KAP1	chr19:44980176-44982083	U2OS	brain:	n/a	n/a
46	ZNF274	chr19:44980289-44981979	GM12878	blood:	n/a	n/a
47	MAX	chr19:44980564-44981796	A549	lung:	n/a	n/a
48	USF1	chr19:44980481-44981828	A549	lung:	n/a	n/a
49	ZNF274	chr19:44979731-44982378	H1-hESC	embryonic stem cell:	n/a	n/a
50	TCF12	chr19:44980462-44981887	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44765918..44767537-chr19:44979922..44981810,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267242	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10401549	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10402815	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10402981	1.00[JPT][hapmap]
rs10406819	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10407028	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10407556	1.00[JPT][hapmap]
rs10407887	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10421647	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10422909	0.89[AMR][1000 genomes]
rs13345032	1.00[JPT][hapmap]
rs1465723	1.00[JPT][hapmap]
rs16959164	0.88[JPT][hapmap]
rs16979124	0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16979134	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16979139	1.00[ASW][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16979226	0.86[JPT][hapmap]
rs1897822	0.91[ASN][1000 genomes]
rs1897824	0.93[ASN][1000 genomes]
rs2117384	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2140112	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2461534	0.86[ASN][1000 genomes]
rs2571040	0.86[ASN][1000 genomes]
rs2571046	0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs2571048	0.86[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs2571049	0.86[ASN][1000 genomes]
rs2571050	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2686758	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2686762	0.98[ASN][1000 genomes]
rs28428189	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28507279	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28576758	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3786496	1.00[JPT][hapmap]
rs4297799	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56787156	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs926020	0.86[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912112	chr19:44853707-45011727	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv912114	chr19:44858776-45002563	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1061350	chr19:44869075-45035469	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv912115	chr19:44957508-44995990	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv960853	chr19:44958445-44982821	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv978867	chr19:44963452-44982821	ZNF genes & repeats Strong transcription Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44966800-44992400	ZNF genes & repeats	Liver	Liver
2	chr19:44967200-44992800	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:44969800-44992200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:44971600-44992200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:44972600-44992200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
6	chr19:44975200-44992200	ZNF genes & repeats	Fetal Brain Female	brain
7	chr19:44975400-44992200	ZNF genes & repeats	Brain Hippocampus Middle	brain
8	chr19:44975600-44990000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:44975600-44992200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
10	chr19:44975800-44992200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
11	chr19:44975800-44992200	ZNF genes & repeats	Brain Anterior Caudate	brain
12	chr19:44976000-44992400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
13	chr19:44976400-44992000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:44976400-44992000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
15	chr19:44976600-44992000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
16	chr19:44976600-44992200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
17	chr19:44976600-44992200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
18	chr19:44976600-44992400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
19	chr19:44977000-44989800	ZNF genes & repeats	Brain Angular Gyrus	brain
20	chr19:44977000-44990200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
21	chr19:44977000-44992000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:44977000-44992200	ZNF genes & repeats	Brain Cingulate Gyrus	brain
23	chr19:44977000-44992200	ZNF genes & repeats	Brain Substantia Nigra	brain
24	chr19:44977000-44992400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
25	chr19:44977000-44992400	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
26	chr19:44977200-44987600	ZNF genes & repeats	Left Ventricle	heart
27	chr19:44977200-44991800	ZNF genes & repeats	Colon Smooth Muscle	Colon
28	chr19:44977200-44992000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
29	chr19:44977200-44992000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
30	chr19:44977200-44992200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
31	chr19:44977200-44992800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:44977400-44987600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:44977400-44989600	ZNF genes & repeats	Right Ventricle	heart
34	chr19:44977400-44990000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:44977400-44992000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
36	chr19:44977400-44992200	ZNF genes & repeats	Fetal Lung	lung
37	chr19:44977400-44992400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
38	chr19:44977400-44992400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:44977600-44981600	ZNF genes & repeats	Right Atrium	heart
40	chr19:44977600-44989800	ZNF genes & repeats	Ovary	ovary
41	chr19:44977600-44992000	ZNF genes & repeats	Primary T cells from cord blood	blood
42	chr19:44977600-44992200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr19:44977800-44989200	ZNF genes & repeats	NH-A	brain
44	chr19:44977800-44989600	ZNF genes & repeats	Fetal Brain Male	brain
45	chr19:44977800-44992000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
46	chr19:44977800-44992000	ZNF genes & repeats	Brain Germinal Matrix	brain
47	chr19:44977800-44992200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:44977800-44992200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:44977800-44992600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
50	chr19:44977800-44992600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood

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