Variant report

Variant	rs16976889
Chromosome Location	chr19:44406443-44406444
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	MAX	chr19:44405671-44406512	HepG2	liver:	n/a	n/a
2	ELK1	chr19:44405822-44406560	GM12878	blood:	n/a	n/a
3	STAT3	chr19:44406348-44406445	GM12878	blood:	n/a	n/a
4	SETDB1	chr19:44405754-44406735	U2OS	brain:	n/a	chr19:44406000-44406024
5	GABPA	chr19:44405553-44406446	SK-N-SH	brain:	n/a	chr19:44406045-44406054
6	MAX	chr19:44405652-44406453	SK-N-SH	brain:	n/a	n/a
7	GABPA	chr19:44405485-44406529	MCF-7	breast:	n/a	chr19:44406045-44406054
8	E2F6	chr19:44405719-44406498	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr19:44405622-44406503	HepG2	liver:	n/a	n/a
10	KAP1	chr19:44405688-44406522	U2OS	brain:	n/a	n/a
11	YY1	chr19:44405656-44406599	SK-N-SH	brain:	n/a	chr19:44406049-44406061
12	MAX	chr19:44405765-44406465	SK-N-SH	brain:	n/a	n/a
13	MAX	chr19:44405784-44406452	A549	lung:	n/a	n/a
14	CEBPB	chr19:44406330-44406569	HepG2	liver:	n/a	chr19:44406441-44406452
15	MAX	chr19:44405502-44406532	A549	lung:	n/a	n/a
16	CEBPB	chr19:44406009-44406568	K562	blood:	n/a	chr19:44406441-44406452

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44405165..44406844-chr19:44438913..44440753,2	K562	blood:

Variant related genes	Relation type
ZNF404	TF binding region
ENSG00000267058	TF binding region
ENSG00000124459	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1124737	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16976860	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16976861	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16976863	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs17449078	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2191562	0.91[YRI][hapmap]
rs2191563	0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56870791	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs59935787	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs60582855	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61022716	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs61277064	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61528694	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6509121	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7254625	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs766959	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs8103693	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs8105412	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs8106317	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs8107364	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs8108832	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458710	chr19:44339960-44410846	Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv579853	chr19:44339960-44410846	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv912108	chr19:44358761-44435167	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44404000-44434800	ZNF genes & repeats	Liver	Liver
2	chr19:44404200-44407000	ZNF genes & repeats	GM12878-XiMat	blood
3	chr19:44404800-44406600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:44404800-44406800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
5	chr19:44405200-44406600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr19:44405200-44406600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:44405200-44406600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:44405200-44406600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:44405200-44406600	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr19:44405200-44406600	Active TSS	Brain Substantia Nigra	brain
11	chr19:44405200-44406600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr19:44405200-44406600	Active TSS	NHLF	lung
13	chr19:44405200-44406800	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr19:44405200-44406800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:44405200-44406800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
16	chr19:44405200-44406800	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr19:44405200-44406800	ZNF genes & repeats	A549	lung
18	chr19:44405200-44406800	ZNF genes & repeats	K562	blood
19	chr19:44405400-44406600	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr19:44405400-44406600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr19:44405400-44406600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:44405400-44406600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr19:44405400-44406600	ZNF genes & repeats	Colonic Mucosa	Colon
24	chr19:44405400-44406600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr19:44405400-44406600	Active TSS	NHDF-Ad	bronchial
26	chr19:44405400-44406800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:44405400-44406800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr19:44405400-44406800	Active TSS	Brain Angular Gyrus	brain
29	chr19:44405400-44406800	ZNF genes & repeats	HSMM	muscle
30	chr19:44405600-44406600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr19:44405600-44406600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:44405600-44406600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr19:44405600-44406600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:44405600-44406600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr19:44405600-44406600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:44405600-44406600	Active TSS	Brain Cingulate Gyrus	brain
37	chr19:44405600-44406600	Active TSS	Left Ventricle	heart
38	chr19:44405600-44406600	Active TSS	Osteobl	bone
39	chr19:44405600-44406800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr19:44405600-44406800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
41	chr19:44405600-44406800	Active TSS	Brain Anterior Caudate	brain
42	chr19:44405600-44407000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr19:44405600-44407000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:44405600-44407000	Active TSS	Fetal Brain Male	brain
45	chr19:44405800-44406600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr19:44405800-44406600	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr19:44405800-44406600	Active TSS	Fetal Kidney	kidney
48	chr19:44405800-44406600	Active TSS	Psoas Muscle	Psoas
49	chr19:44405800-44406600	Active TSS	NHEK	skin
50	chr19:44405800-44407000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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