Variant report

Variant	rs29730
Chromosome Location	chr19:21371001-21371002
allele	A/G
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	POLR2A	chr19:21370686-21371030	K562	blood:	n/a	n/a
2	POLR2A	chr19:21370729-21371137	K562	blood:	n/a	n/a
3	POLR2A	chr19:21370871-21371039	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:21366577-21374844	K562	blood:	n/a	n/a
5	POLR2A	chr19:21370378-21371040	K562	blood:	n/a	n/a

Variant related genes	Relation type
VN1R82P	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11672526	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs250001	0.84[EUR][1000 genomes]
rs25760	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs29701	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29702	0.96[EUR][1000 genomes]
rs29704	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29706	0.96[EUR][1000 genomes]
rs29709	0.94[EUR][1000 genomes]
rs29710	0.96[EUR][1000 genomes]
rs29711	0.96[EUR][1000 genomes]
rs29712	0.95[EUR][1000 genomes]
rs29713	0.96[EUR][1000 genomes]
rs29714	0.96[EUR][1000 genomes]
rs29716	0.95[EUR][1000 genomes]
rs29717	0.95[EUR][1000 genomes]
rs29721	0.96[EUR][1000 genomes]
rs29723	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29724	0.89[ASN][1000 genomes]
rs29726	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs29727	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs459620	0.95[EUR][1000 genomes]
rs466262	0.94[EUR][1000 genomes]
rs467187	0.94[EUR][1000 genomes]
rs62108173	0.84[EUR][1000 genomes]
rs62124917	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62124923	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62124924	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250372	0.85[CEU][hapmap]
rs7259520	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73026700	0.95[ASN][1000 genomes]
rs73028504	0.95[ASN][1000 genomes]
rs8101995	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630897	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs29730	ZNF708	cis	Muscle Skeletal	GTEx
rs29730	ZNF708	cis	lung	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21333000-21373000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:21360000-21371200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:21360400-21371200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr19:21363800-21372000	Weak transcription	Gastric	stomach
5	chr19:21363800-21374000	Weak transcription	Pancreas	Pancrea
6	chr19:21365200-21373200	Strong transcription	HSMM	muscle
7	chr19:21365800-21374400	Weak transcription	Hela-S3	cervix
8	chr19:21366200-21371200	Strong transcription	Dnd41	blood
9	chr19:21366400-21380400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:21367000-21371600	Weak transcription	Fetal Kidney	kidney
11	chr19:21367000-21377200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr19:21367000-21377800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:21367000-21379200	Weak transcription	Ovary	ovary
14	chr19:21367000-21380600	Weak transcription	Placenta	Placenta
15	chr19:21367200-21371600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr19:21367200-21374400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:21367200-21374400	Weak transcription	Fetal Muscle Leg	muscle
18	chr19:21367200-21375600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr19:21367200-21377600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:21367200-21377600	Weak transcription	Left Ventricle	heart
21	chr19:21367400-21371400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr19:21367400-21372200	Weak transcription	NH-A	brain
23	chr19:21367400-21379800	Weak transcription	K562	blood
24	chr19:21367800-21373800	Weak transcription	HSMMtube	muscle
25	chr19:21368400-21372000	Weak transcription	Primary B cells from cord blood	blood
26	chr19:21368400-21373200	Weak transcription	Primary T cells from cord blood	blood
27	chr19:21368600-21374600	Weak transcription	Fetal Brain Female	brain
28	chr19:21368600-21374600	Weak transcription	Fetal Lung	lung
29	chr19:21368600-21378000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:21368800-21372000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:21369000-21372000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:21369000-21375800	Weak transcription	Fetal Stomach	stomach
33	chr19:21369200-21372400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr19:21369200-21373200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr19:21369200-21375200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr19:21369400-21374200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:21369400-21374600	Weak transcription	Brain Germinal Matrix	brain
38	chr19:21369600-21371600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:21369600-21377600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr19:21369800-21372200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:21370000-21372200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:21370000-21372400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:21370000-21380000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:21370000-21382200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr19:21370200-21372800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:21370200-21374400	Weak transcription	Thymus	Thymus
47	chr19:21370200-21377600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr19:21370200-21381000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:21370600-21371200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:21370600-21374000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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