Variant report

Variant	rs16975684
Chromosome Location	chr19:42706310-42706311
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42699563..42702889-chr19:42705944..42708655,3	K562	blood:
2	chr19:42704086..42706332-chr19:42793482..42795318,2	K562	blood:
3	chr19:42705013..42706580-chr19:42758213..42760706,2	MCF-7	breast:
4	chr19:42705772..42709230-chr19:42709597..42712462,3	MCF-7	breast:
5	chr19:42699563..42702777-chr19:42704104..42708655,4	K562	blood:
6	chr19:42705928..42708384-chr19:42729085..42731992,2	MCF-7	breast:
7	chr19:42705382..42709169-chr19:42719757..42723550,6	K562	blood:
8	chr19:42703977..42706595-chr19:42745601..42747627,2	K562	blood:
9	chr19:42704957..42708119-chr19:42733053..42736266,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204957	Chromatin interaction
ENSG00000268643	Chromatin interaction
ENSG00000028277	Chromatin interaction
ENSG00000105723	Chromatin interaction
ENSG00000160570	Chromatin interaction
ENSG00000105722	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10410185	0.82[CHB][hapmap]
rs10410198	0.82[CHB][hapmap]
rs10410698	0.82[CHB][hapmap]
rs10500285	0.93[GIH][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs11878620	0.93[GIH][hapmap];0.80[MEX][hapmap]
rs11880124	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11883412	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1206009	0.82[CHB][hapmap]
rs1206027	0.82[CHB][hapmap]
rs1206029	0.82[CHB][hapmap]
rs1206033	0.82[CHB][hapmap]
rs1206038	0.82[CHB][hapmap]
rs1206040	0.82[CHB][hapmap]
rs1206041	0.82[CHB][hapmap]
rs1206044	0.82[CHB][hapmap]
rs12232804	0.82[EUR][1000 genomes]
rs1613100	0.82[CHB][hapmap]
rs1654623	0.82[CHB][hapmap]
rs1676211	0.82[CHB][hapmap]
rs1676217	0.82[CHB][hapmap]
rs1676221	0.82[CHB][hapmap]
rs1676222	0.82[CHB][hapmap]
rs1685565	0.82[CHB][hapmap]
rs16975663	0.80[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]
rs17270057	0.82[EUR][1000 genomes]
rs17270169	0.89[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs17342179	0.82[EUR][1000 genomes]
rs17342284	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs17750207	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2267630	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs2302485	0.93[GIH][hapmap];0.80[MEX][hapmap]
rs2303652	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2537697	0.82[CHB][hapmap]
rs2615614	0.82[CHB][hapmap]
rs28621009	0.82[CHB][hapmap]
rs3736109	0.80[CEU][hapmap];1.00[YRI][hapmap]
rs3745231	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3745233	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810148	0.82[CHB][hapmap];0.90[MKK][hapmap]
rs3810151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3826705	0.89[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs3826706	1.00[YRI][hapmap]
rs4141062	0.82[CHB][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap]
rs59099214	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62119628	0.86[ASN][1000 genomes]
rs7248379	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.95[ASN][1000 genomes]
rs7251466	0.89[CEU][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap]
rs741070	0.82[CHB][hapmap]
rs8108096	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8182491	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs851296	0.82[CHB][hapmap]
rs899661	0.80[CEU][hapmap];0.87[TSI][hapmap]
rs9636121	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
7	nsv833833	chr19:42657276-42783122	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16975684	ZNF219	trans	lymphoblastoid	RTeQTL
rs16975684	DEDD2	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42696600-42710000	Weak transcription	NH-A	brain
2	chr19:42696600-42712200	Weak transcription	Fetal Kidney	kidney
3	chr19:42697800-42706800	Weak transcription	Ovary	ovary
4	chr19:42697800-42708800	Weak transcription	NHDF-Ad	bronchial
5	chr19:42697800-42710400	Weak transcription	HSMMtube	muscle
6	chr19:42698000-42707600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:42698000-42709800	Weak transcription	HSMM	muscle
8	chr19:42698600-42709800	Weak transcription	HUVEC	blood vessel
9	chr19:42699800-42714000	Weak transcription	Fetal Brain Male	brain
10	chr19:42700200-42708200	Genic enhancers	Spleen	Spleen
11	chr19:42700200-42714600	Strong transcription	Brain Germinal Matrix	brain
12	chr19:42700400-42710400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:42700400-42714600	Strong transcription	Stomach Smooth Muscle	stomach
14	chr19:42700400-42717200	Weak transcription	Psoas Muscle	Psoas
15	chr19:42700400-42719800	Strong transcription	Fetal Stomach	stomach
16	chr19:42701000-42707200	Genic enhancers	Rectal Mucosa Donor 31	rectum
17	chr19:42701000-42709000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:42701000-42720200	Weak transcription	Fetal Heart	heart
19	chr19:42701200-42706400	Strong transcription	Placenta Amnion	Placenta Amnion
20	chr19:42701200-42715200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:42701200-42719800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:42701400-42714400	Strong transcription	Brain Angular Gyrus	brain
23	chr19:42701400-42715200	Strong transcription	Fetal Brain Female	brain
24	chr19:42701600-42708600	Strong transcription	Pancreas	Pancrea
25	chr19:42701600-42708800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:42701600-42710800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:42701600-42715200	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr19:42701800-42707200	Strong transcription	Liver	Liver
29	chr19:42702000-42708400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr19:42702000-42709000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:42702000-42710400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:42702000-42710400	Strong transcription	A549	lung
33	chr19:42702000-42711000	Strong transcription	Gastric	stomach
34	chr19:42702000-42714200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:42702000-42715200	Strong transcription	Fetal Intestine Large	intestine
36	chr19:42702000-42719400	Strong transcription	Fetal Intestine Small	intestine
37	chr19:42702200-42706600	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr19:42702200-42708400	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr19:42702200-42711200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr19:42702200-42714400	Strong transcription	Aorta	Aorta
41	chr19:42702400-42707800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:42702400-42708600	Strong transcription	NHLF	lung
43	chr19:42702400-42709000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr19:42702400-42709800	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr19:42702400-42710800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:42702400-42714400	Strong transcription	Brain Cingulate Gyrus	brain
47	chr19:42702400-42714400	Strong transcription	HepG2	liver
48	chr19:42702400-42714600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:42702400-42714600	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr19:42702800-42706400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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