Variant report

Variant	rs2972655
Chromosome Location	chr19:36818055-36818056
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	chr19:36817485-36819387	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:36817596-36818097	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:36817752-36818280	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:36817974-36818127	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
LINC00665	TF binding region
ENSG00000222730	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10418925	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11084855	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11084857	0.81[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1127406	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1129375	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1129376	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11882601	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12460237	0.91[CHB][hapmap]
rs12609058	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap]
rs17206365	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs17639740	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2432048	0.90[CHB][hapmap]
rs2432053	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs2432055	0.91[CHB][hapmap]
rs2910681	0.91[CHB][hapmap]
rs2918325	0.83[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2918350	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2918352	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2918353	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2918354	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2918362	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2918363	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2918366	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2918367	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2918371	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2918374	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918377	0.91[CHB][hapmap]
rs2918384	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2967485	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967486	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967487	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967488	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967490	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967491	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967492	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967494	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967495	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967498	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967499	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967502	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967503	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2972533	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2972540	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs2972630	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972631	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2972634	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2972635	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972636	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972637	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972638	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2972643	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972650	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972654	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34636215	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs34723481	0.85[ASN][1000 genomes]
rs35007948	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35822095	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4806320	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57488812	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58192477	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60499535	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60842204	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62112620	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62112621	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62112627	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62112629	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62112634	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6510528	0.86[CHB][hapmap]
rs73043854	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7343105	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8111845	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8113638	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520020	chr19:36721368-36822594	Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1063208	chr19:36743461-36847486	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1056901	chr19:36749658-36847486	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1061054	chr19:36751703-36847486	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1055260	chr19:36752221-36847486	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1056850	chr19:36752663-36847486	Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1064983	chr19:36752663-36847625	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1057579	chr19:36752663-36847822	Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv1825146	chr19:36800927-36846993	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1837043	chr19:36800927-36846993	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv2474	chr19:36804469-36865415	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv2763143	chr19:36805705-36847498	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1059568	chr19:36806475-36847864	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv1823621	chr19:36807288-36845863	Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1064343	chr19:36807288-36853102	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	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
rs2972655	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs2972655	LOC284412	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36800800-36822000	Weak transcription	Psoas Muscle	Psoas
2	chr19:36804000-36820600	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr19:36804800-36820800	Weak transcription	Brain Angular Gyrus	brain
4	chr19:36805400-36822000	Weak transcription	HSMMtube	muscle
5	chr19:36805800-36821000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:36806400-36820600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:36806600-36821000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:36806600-36822000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr19:36806800-36820000	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr19:36808600-36820000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:36810000-36820200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:36810400-36820800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr19:36810600-36820600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:36812800-36818400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:36812800-36818800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:36812800-36821600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
17	chr19:36813200-36821000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr19:36813200-36821800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:36813400-36819200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:36813400-36821400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:36813400-36821800	Weak transcription	Brain Substantia Nigra	brain
22	chr19:36813600-36821800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:36814000-36819600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:36814600-36821000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:36814800-36820600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:36814800-36820800	Strong transcription	Brain Germinal Matrix	brain
27	chr19:36814800-36821400	Strong transcription	Fetal Muscle Leg	muscle
28	chr19:36815200-36821000	Strong transcription	Fetal Brain Female	brain
29	chr19:36815200-36822000	Weak transcription	NHLF	lung
30	chr19:36815400-36821200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr19:36815400-36822000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr19:36815800-36818200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:36815800-36818200	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr19:36815800-36818200	Strong transcription	NHEK	skin
35	chr19:36815800-36820200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:36815800-36821000	Strong transcription	Fetal Stomach	stomach
37	chr19:36815800-36821200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:36815800-36821400	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr19:36815800-36821400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:36815800-36821800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:36816200-36819000	Weak transcription	Fetal Thymus	thymus
42	chr19:36816200-36819400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr19:36816200-36821000	Weak transcription	HSMM	muscle
44	chr19:36816200-36821400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
45	chr19:36816400-36818200	Strong transcription	Adipose Nuclei	Adipose
46	chr19:36816400-36818200	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr19:36816400-36818200	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr19:36816400-36818400	Strong transcription	Brain Cingulate Gyrus	brain
49	chr19:36816400-36819400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:36816400-36819400	ZNF genes & repeats	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links