Variant report

Variant	rs899661
Chromosome Location	chr19:42542466-42542467
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42540941..42542616-chr19:42544852..42547771,2	MCF-7	breast:
2	chr19:42535754..42538342-chr19:42542114..42544561,2	K562	blood:

Variant related genes	Relation type
ENSG00000105737	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10407506	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[MKK][hapmap];0.93[ASN][1000 genomes]
rs10500285	0.83[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes]
rs11878917	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11880124	0.91[TSI][hapmap]
rs11883412	0.96[TSI][hapmap]
rs12232804	0.87[AMR][1000 genomes]
rs16975663	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap]
rs16975684	0.80[CEU][hapmap];0.87[TSI][hapmap]
rs17270057	0.87[AMR][1000 genomes]
rs17270169	0.90[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes]
rs17342067	0.85[AMR][1000 genomes]
rs17342179	0.87[AMR][1000 genomes]
rs17342284	0.88[CEU][hapmap];0.85[CHB][hapmap];0.87[AMR][1000 genomes]
rs2217342	0.91[TSI][hapmap]
rs2303652	0.87[TSI][hapmap]
rs3736109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3745231	0.87[TSI][hapmap]
rs3810151	0.80[CEU][hapmap]
rs3826705	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs407096	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs443239	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs454150	0.91[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803520	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61195828	0.93[ASN][1000 genomes]
rs7248379	0.80[CEU][hapmap];0.87[TSI][hapmap]
rs7251466	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7253767	0.85[AMR][1000 genomes]
rs7253791	0.85[AMR][1000 genomes]
rs7253915	0.85[AMR][1000 genomes]
rs8106871	0.85[AMR][1000 genomes]
rs8182491	0.80[CEU][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription 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 miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs899661	ZNF219	trans	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42511000-42542600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:42528400-42553000	Weak transcription	Spleen	Spleen
3	chr19:42533000-42545800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:42535600-42555200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:42536800-42546200	Weak transcription	Brain Angular Gyrus	brain
6	chr19:42537000-42553200	Weak transcription	Colon Smooth Muscle	Colon
7	chr19:42537000-42557200	Weak transcription	Fetal Kidney	kidney
8	chr19:42537200-42558600	Weak transcription	Brain Hippocampus Middle	brain
9	chr19:42538600-42547400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr19:42539000-42547000	Strong transcription	Brain Germinal Matrix	brain
11	chr19:42539000-42556400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:42539400-42545200	Weak transcription	Fetal Brain Male	brain
13	chr19:42539400-42570200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:42539400-42572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:42539600-42544200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr19:42540000-42547800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:42540400-42547600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr19:42540400-42572600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr19:42540600-42543800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr19:42540600-42545200	Strong transcription	Fetal Brain Female	brain
21	chr19:42540600-42547400	Strong transcription	Fetal Stomach	stomach
22	chr19:42540600-42550800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:42540600-42551000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:42540600-42551600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:42540800-42547200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr19:42540800-42551000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr19:42540800-42551800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:42541000-42542800	Enhancers	Right Ventricle	heart
29	chr19:42541200-42543800	Enhancers	Fetal Heart	heart
30	chr19:42541200-42544200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:42541600-42543800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr19:42541600-42546600	Strong transcription	Brain Anterior Caudate	brain
33	chr19:42541600-42547200	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr19:42541800-42542600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:42541800-42542600	Strong transcription	Rectal Smooth Muscle	rectum
36	chr19:42541800-42542600	Enhancers	Right Atrium	heart
37	chr19:42541800-42542800	Enhancers	Left Ventricle	heart
38	chr19:42541800-42543200	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr19:42541800-42547200	Strong transcription	Aorta	Aorta
40	chr19:42541800-42551200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr19:42542000-42543400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr19:42542000-42543800	Strong transcription	Primary hematopoietic stem cells	blood
43	chr19:42542000-42547200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:42542200-42542800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr19:42542200-42543400	Enhancers	Fetal Muscle Trunk	muscle
46	chr19:42542200-42543400	Enhancers	Fetal Muscle Leg	muscle
47	chr19:42542400-42542800	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr19:42542400-42542800	Enhancers	HSMMtube	muscle
49	chr19:42542400-42543400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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