Variant report

Variant	rs2972540
Chromosome Location	chr19:36730960-36730961
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36729380..36732375-chr19:36732759..36734481,3	MCF-7	breast:
2	chr19:36729552..36731662-chr19:36736640..36739209,2	K562	blood:
3	chr19:36729000..36731636-chr19:36732341..36735804,4	K562	blood:
4	chr19:36730136..36732594-chr19:36734296..36737243,2	K562	blood:

Variant related genes	Relation type
ENSG00000196357	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10416729	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10418925	0.82[CHB][hapmap]
rs11084857	0.89[CHD][hapmap]
rs1127406	0.85[CEU][hapmap]
rs1129375	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs1129376	0.84[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[TSI][hapmap]
rs11673662	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11882601	0.84[CEU][hapmap]
rs12460237	0.81[CHB][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap];0.89[ASN][1000 genomes]
rs12608941	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12609058	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs17206365	0.88[CEU][hapmap]
rs17639740	0.82[CHB][hapmap]
rs1898675	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2432040	0.94[ASN][1000 genomes]
rs2432044	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2432046	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2432048	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2432050	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2432053	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432055	0.93[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap]
rs2438515	0.93[ASN][1000 genomes]
rs2438516	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2910681	0.93[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2918322	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2918323	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2918324	0.84[ASN][1000 genomes]
rs2918325	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2918328	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2918376	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918377	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2918381	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2918382	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2918383	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2918384	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967490	0.84[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.86[TSI][hapmap]
rs2967491	0.84[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.86[TSI][hapmap]
rs2972320	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972530	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2972532	0.84[ASN][1000 genomes]
rs2972533	0.96[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972534	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972535	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972536	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972543	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2972630	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs2972631	0.81[CHB][hapmap]
rs2972643	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs2972654	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs2972655	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs34912665	0.87[ASN][1000 genomes]
rs4293497	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4315447	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs57614488	0.84[ASN][1000 genomes]
rs57890739	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6510528	0.80[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.86[ASN][1000 genomes]
rs8107260	0.86[ASN][1000 genomes]
rs8107616	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	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
4	nsv9715	chr19:36729688-36811749	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2972540	ZNF545	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36707600-36731800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:36710000-36732200	ZNF genes & repeats	A549	lung
3	chr19:36710000-36732200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:36714000-36731000	Strong transcription	Dnd41	blood
5	chr19:36714400-36731400	ZNF genes & repeats	Liver	Liver
6	chr19:36715200-36731200	Strong transcription	Fetal Brain Female	brain
7	chr19:36715200-36731600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
8	chr19:36716600-36731400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr19:36718400-36731800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:36719400-36731400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:36719400-36731600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
12	chr19:36721000-36735800	Weak transcription	Right Atrium	heart
13	chr19:36724400-36735800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:36724800-36731400	Strong transcription	Placenta	Placenta
15	chr19:36726600-36731400	ZNF genes & repeats	Fetal Muscle Leg	muscle
16	chr19:36728200-36731200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:36728200-36731400	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr19:36728200-36732000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr19:36728200-36735800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:36728200-36735800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr19:36728200-36736000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr19:36728400-36731200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:36728400-36735800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr19:36728400-36735800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:36728400-36735800	Weak transcription	Brain Anterior Caudate	brain
26	chr19:36728400-36735800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr19:36728400-36735800	Weak transcription	Brain Substantia Nigra	brain
28	chr19:36728400-36736200	Weak transcription	Gastric	stomach
29	chr19:36728600-36731000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:36728600-36735800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr19:36728600-36735800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr19:36728600-36735800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr19:36728600-36735800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:36728600-36736000	Weak transcription	Left Ventricle	heart
35	chr19:36728600-36736000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:36728800-36731400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr19:36728800-36731400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:36728800-36735800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr19:36728800-36735800	Weak transcription	NHLF	lung
40	chr19:36729000-36731200	Strong transcription	HSMM	muscle
41	chr19:36729000-36734800	Weak transcription	NHEK	skin
42	chr19:36729000-36735800	Weak transcription	Fetal Heart	heart
43	chr19:36729200-36731400	ZNF genes & repeats	Fetal Intestine Large	intestine
44	chr19:36729200-36735800	Weak transcription	Fetal Brain Male	brain
45	chr19:36729200-36735800	Weak transcription	Fetal Kidney	kidney
46	chr19:36729400-36731200	Strong transcription	NH-A	brain
47	chr19:36729400-36731400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr19:36729400-36734200	Weak transcription	NHDF-Ad	bronchial
49	chr19:36729400-36735800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr19:36729400-36735800	Weak transcription	HMEC	breast

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