Variant report

Variant	rs29727
Chromosome Location	chr19:21374305-21374306
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21366435..21372841-chr19:21372957..21377596,6	K562	blood:
2	chr19:21257717..21259573-chr19:21372943..21374798,2	K562	blood:

Variant related genes	Relation type
ENSG00000268995	Chromatin interaction
ENSG00000196705	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs11672526	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[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	0.96[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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29730	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	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62124923	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62124924	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7250372	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs7259520	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73026700	0.84[ASN][1000 genomes]
rs73028504	0.84[ASN][1000 genomes]
rs8101995	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9630897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	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
6	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs29727	ZNF708	cis	cerebellum	SCAN
rs29727	TSSK6	cis	parietal	SCAN
rs29727	TMEM59L	cis	parietal	SCAN
rs29727	ZNF43	cis	parietal	SCAN
rs29727	ZNF708	cis	Muscle Skeletal	GTEx
rs29727	NDUFA13	cis	cerebellum	SCAN
rs29727	ZNF708	cis	lung	GTEx
rs29727	ZNF493	cis	parietal	SCAN
rs29727	ZNF493	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21365800-21374400	Weak transcription	Hela-S3	cervix
2	chr19:21366400-21380400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:21367000-21377200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:21367000-21377800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:21367000-21379200	Weak transcription	Ovary	ovary
6	chr19:21367000-21380600	Weak transcription	Placenta	Placenta
7	chr19:21367200-21374400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:21367200-21374400	Weak transcription	Fetal Muscle Leg	muscle
9	chr19:21367200-21375600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:21367200-21377600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:21367200-21377600	Weak transcription	Left Ventricle	heart
12	chr19:21367400-21379800	Weak transcription	K562	blood
13	chr19:21368600-21374600	Weak transcription	Fetal Brain Female	brain
14	chr19:21368600-21374600	Weak transcription	Fetal Lung	lung
15	chr19:21368600-21378000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:21369000-21375800	Weak transcription	Fetal Stomach	stomach
17	chr19:21369200-21375200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr19:21369400-21374600	Weak transcription	Brain Germinal Matrix	brain
19	chr19:21369600-21377600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr19:21370000-21380000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:21370000-21382200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr19:21370200-21374400	Weak transcription	Thymus	Thymus
23	chr19:21370200-21377600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr19:21370200-21381000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:21370600-21374400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:21370600-21377600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:21370600-21380600	Weak transcription	Fetal Intestine Small	intestine
28	chr19:21370800-21378800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:21371000-21374600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:21371000-21377600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:21372200-21374600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:21372800-21374600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:21372800-21374600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:21372800-21380400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:21373000-21374400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:21373000-21375800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:21373000-21375800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr19:21373000-21380800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:21373200-21377000	Weak transcription	HSMM	muscle
40	chr19:21373200-21381800	Weak transcription	Dnd41	blood
41	chr19:21373400-21376600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:21374000-21374400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links