Variant report

Variant	rs438943
Chromosome Location	chr19:53140562-53140563
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	POLR2A	chr19:53140111-53142148	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:53140135-53142012	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:53140366-53142176	GM12892	blood:	n/a	n/a
4	CTCF	chr19:53140420-53140570	Caco-2	colon:	n/a	n/a
5	POLR2A	chr19:53140421-53141697	GM12892	blood:	n/a	n/a
6	POLR2A	chr19:53139933-53142093	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:53140472-53140603	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:53140485-53140727	GM12878	blood:	n/a	n/a
9	HEY1	chr19:53140110-53140804	K562	blood:	n/a	n/a
10	POLR2A	chr19:53140028-53140709	K562	blood:	n/a	n/a
11	POLR2A	chr19:53140397-53142088	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53139623..53144311-chr19:53192220..53194807,4	MCF-7	breast:
2	chr19:53140133..53142689-chr19:53604558..53606639,2	MCF-7	breast:

Variant related genes	Relation type
ZNF83	TF binding region
ENSG00000167766	Chromatin interaction
ENSG00000170949	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs189082	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs193039	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs329941	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs329952	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs329958	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs329959	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs329960	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs329961	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs329962	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs329963	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3745105	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3745106	0.92[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs406232	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs410857	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs472389	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs475188	0.92[CEU][hapmap];0.89[GIH][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs476955	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs484919	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs619872	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs639767	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs681090	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7255536	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7255970	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7256179	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7259344	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7259397	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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	nsv912305	chr19:53092465-53349850	Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv912306	chr19:53092465-53400760	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv912307	chr19:53092465-53433054	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv912311	chr19:53103875-53212361	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv912312	chr19:53103875-53296371	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv912313	chr19:53103875-53436337	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv912314	chr19:53105547-53144082	Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv912315	chr19:53105547-53149967	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
14	nsv912316	chr19:53105547-53158023	Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
15	nsv912317	chr19:53105547-53440653	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv1066762	chr19:53112568-53552217	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
17	nsv912318	chr19:53118278-53451291	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
18	nsv458744	chr19:53120559-53236331	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
19	nsv580028	chr19:53120559-53236331	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
20	esv3489404	chr19:53121944-53391394	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
21	esv3489405	chr19:53121944-53391394	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
22	nsv1066876	chr19:53123577-53157096	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv580029	chr19:53137583-53164172	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs438943	VN1R1	cis	cerebellum	SCAN
rs438943	TNNI3	cis	parietal	SCAN
rs438943	ZNF83	cis	multi-tissue	Pritchard
rs438943	RPS9	cis	cerebellum	SCAN
rs438943	ZNF83	cis	lymphoblastoid	seeQTL
rs438943	AURKC	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53121200-53140800	Weak transcription	HSMMtube	muscle
2	chr19:53121600-53140800	Weak transcription	Brain Angular Gyrus	brain
3	chr19:53125000-53140600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr19:53127000-53140800	Weak transcription	Ovary	ovary
5	chr19:53129000-53140600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:53129200-53140600	Weak transcription	Colonic Mucosa	Colon
7	chr19:53129200-53140800	Weak transcription	Small Intestine	intestine
8	chr19:53129600-53140600	Weak transcription	HSMM	muscle
9	chr19:53130000-53140600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr19:53130000-53140800	Weak transcription	Aorta	Aorta
11	chr19:53130400-53140800	Weak transcription	Left Ventricle	heart
12	chr19:53130600-53140800	Weak transcription	Fetal Brain Female	brain
13	chr19:53130600-53140800	Weak transcription	Psoas Muscle	Psoas
14	chr19:53131200-53140600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr19:53132200-53140600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:53132600-53140600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:53132800-53140600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:53134200-53140600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr19:53135800-53140600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr19:53137600-53140600	Weak transcription	Esophagus	oesophagus
21	chr19:53137800-53140800	Weak transcription	Fetal Intestine Large	intestine
22	chr19:53138400-53140600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr19:53138400-53140800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr19:53138600-53140600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:53138800-53140600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:53138800-53140600	Weak transcription	Gastric	stomach
27	chr19:53139600-53140600	Enhancers	Primary B cells from peripheral blood	blood
28	chr19:53139600-53140600	Enhancers	Thymus	Thymus
29	chr19:53139800-53142000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:53140000-53140600	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr19:53140000-53140800	Enhancers	Lung	lung
32	chr19:53140000-53140800	Enhancers	Placenta Amnion	Placenta Amnion
33	chr19:53140200-53140600	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr19:53140200-53140600	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr19:53140200-53140600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr19:53140200-53140600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:53140200-53140600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:53140200-53140600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr19:53140200-53140600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr19:53140200-53140600	Enhancers	Hela-S3	cervix
41	chr19:53140200-53140600	Enhancers	K562	blood
42	chr19:53140200-53140600	Enhancers	NHEK	skin
43	chr19:53140200-53140800	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr19:53140200-53140800	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr19:53140200-53140800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr19:53140200-53140800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr19:53140200-53140800	Enhancers	Brain Germinal Matrix	brain
48	chr19:53140200-53140800	Enhancers	HepG2	liver
49	chr19:53140200-53140800	Enhancers	NHDF-Ad	bronchial
50	chr19:53140200-53141200	Flanking Active TSS	Dnd41	blood

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