Variant report

Variant	rs16997503
Chromosome Location	chr19:21370630-21370631
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	STAT3	chr19:21370601-21370774	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr19:21366577-21374844	K562	blood:	n/a	n/a
3	POLR2A	chr19:21370378-21371040	K562	blood:	n/a	n/a

Variant related genes	Relation type
VN1R82P	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10406253	0.90[CEU][hapmap]
rs11881107	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12052171	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12151204	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17445374	1.00[CEU][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17445381	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2115498	0.95[CEU][hapmap];0.96[TSI][hapmap]
rs57941450	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58095420	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59436607	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60870377	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6511202	0.95[CEU][hapmap];0.96[TSI][hapmap]
rs6511204	0.95[CEU][hapmap];0.96[TSI][hapmap]
rs6511205	0.95[CEU][hapmap]
rs67716442	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7256860	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73028563	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73028565	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73028577	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8101918	0.94[CEU][hapmap]
rs995655	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv960811	chr19:21200306-21371757	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3399352	chr19:21232738-21423323	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv911414	chr19:21355473-21454672	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs16997503	ZNF738	cis	parietal	SCAN
rs16997503	ZNF714	cis	cerebellum	SCAN
rs16997503	ZNF429	cis	multi-tissue	Pritchard
rs16997503	ZNF429	cis	cerebellum	SCAN
rs16997503	ZNF100	cis	cerebellum	SCAN
rs16997503	RPSAP58	cis	cerebellum	SCAN
rs16997503	ZNF714	cis	parietal	SCAN
rs16997503	ZNF429	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21331000-21371000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:21333000-21373000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:21355200-21370800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:21355200-21371000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:21360000-21371200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:21360400-21371200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr19:21363800-21372000	Weak transcription	Gastric	stomach
8	chr19:21363800-21374000	Weak transcription	Pancreas	Pancrea
9	chr19:21365200-21373200	Strong transcription	HSMM	muscle
10	chr19:21365800-21374400	Weak transcription	Hela-S3	cervix
11	chr19:21366200-21371200	Strong transcription	Dnd41	blood
12	chr19:21366400-21380400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:21366800-21371000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:21367000-21370800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:21367000-21371600	Weak transcription	Fetal Kidney	kidney
16	chr19:21367000-21377200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:21367000-21377800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr19:21367000-21379200	Weak transcription	Ovary	ovary
19	chr19:21367000-21380600	Weak transcription	Placenta	Placenta
20	chr19:21367200-21371600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr19:21367200-21374400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:21367200-21374400	Weak transcription	Fetal Muscle Leg	muscle
23	chr19:21367200-21375600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr19:21367200-21377600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:21367200-21377600	Weak transcription	Left Ventricle	heart
26	chr19:21367400-21370800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:21367400-21371400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:21367400-21372200	Weak transcription	NH-A	brain
29	chr19:21367400-21379800	Weak transcription	K562	blood
30	chr19:21367800-21373800	Weak transcription	HSMMtube	muscle
31	chr19:21368400-21372000	Weak transcription	Primary B cells from cord blood	blood
32	chr19:21368400-21373200	Weak transcription	Primary T cells from cord blood	blood
33	chr19:21368600-21374600	Weak transcription	Fetal Brain Female	brain
34	chr19:21368600-21374600	Weak transcription	Fetal Lung	lung
35	chr19:21368600-21378000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:21368800-21372000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:21369000-21372000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:21369000-21375800	Weak transcription	Fetal Stomach	stomach
39	chr19:21369200-21372400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr19:21369200-21373200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr19:21369200-21375200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr19:21369400-21374200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr19:21369400-21374600	Weak transcription	Brain Germinal Matrix	brain
44	chr19:21369600-21371000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr19:21369600-21371600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:21369600-21377600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr19:21369800-21370800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
48	chr19:21369800-21372200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr19:21370000-21371000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr19:21370000-21371000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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