Variant report

Variant	rs172956
Chromosome Location	chr19:53015864-53015865
allele	A/C
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	chr19:53015620-53016213	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:53015682-53016169	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000269349	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11084170	0.88[ASN][1000 genomes]
rs11669969	0.87[ASN][1000 genomes]
rs12610532	0.94[ASN][1000 genomes]
rs12984325	0.87[ASN][1000 genomes]
rs161930	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs161932	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1677467	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011702	0.87[ASN][1000 genomes]
rs2115372	0.81[ASN][1000 genomes]
rs2868688	0.80[ASN][1000 genomes]
rs324745	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324747	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324748	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs326441	0.82[JPT][hapmap]
rs326449	0.82[JPT][hapmap]
rs326452	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs326456	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs326458	0.83[JPT][hapmap]
rs329929	0.83[ASN][1000 genomes]
rs329930	0.81[ASN][1000 genomes]
rs378790	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs389503	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs400278	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs414595	0.99[ASN][1000 genomes]
rs414804	0.89[ASN][1000 genomes]
rs419317	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802968	0.94[ASN][1000 genomes]
rs4802969	0.90[ASN][1000 genomes]
rs4802970	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs621469	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633763	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650885	0.91[ASN][1000 genomes]
rs650937	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs666356	0.80[JPT][hapmap]
rs802878	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic 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	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	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
6	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3404701	chr19:52986895-53035152	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1058567	chr19:52992455-53021505	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3440535	chr19:52993529-53035203	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1066717	chr19:52993620-53041995	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1064342	chr19:52996710-53041119	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1055825	chr19:53001299-53037378	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1055859	chr19:53001299-53041119	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1060656	chr19:53001299-53041995	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53002600-53021400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:53003400-53022600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:53003800-53017600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr19:53006400-53021200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:53006400-53021400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:53006600-53016200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:53006800-53021400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr19:53007000-53021400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr19:53009000-53022600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:53011000-53017800	Weak transcription	Right Ventricle	heart
11	chr19:53012200-53016000	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr19:53012400-53016200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr19:53013000-53016000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr19:53013000-53016200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:53013000-53016200	Weak transcription	Fetal Stomach	stomach
16	chr19:53013200-53021800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr19:53013400-53016400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:53013800-53018200	Strong transcription	Fetal Muscle Leg	muscle
19	chr19:53014200-53016000	Strong transcription	Ovary	ovary
20	chr19:53014800-53016400	Strong transcription	Brain Germinal Matrix	brain
21	chr19:53014800-53021200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:53015000-53020600	Strong transcription	Fetal Brain Female	brain
23	chr19:53015400-53017000	Weak transcription	Brain Anterior Caudate	brain
24	chr19:53015400-53018400	Weak transcription	Dnd41	blood
25	chr19:53015400-53029600	Weak transcription	Fetal Brain Male	brain
26	chr19:53015600-53016400	ZNF genes & repeats	Aorta	Aorta
27	chr19:53015600-53017400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr19:53015600-53017600	Weak transcription	HSMMtube	muscle
29	chr19:53015600-53017800	Weak transcription	Fetal Kidney	kidney
30	chr19:53015600-53017800	Weak transcription	Fetal Lung	lung
31	chr19:53015600-53018400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:53015600-53018600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:53015600-53019200	Weak transcription	Brain Angular Gyrus	brain
34	chr19:53015600-53021200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:53015800-53021400	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links