Variant report

Variant	rs2562465
Chromosome Location	chr19:21713895-21713896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1012040	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1021722	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10404462	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10406824	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10406870	0.81[EUR][1000 genomes]
rs10411757	0.83[EUR][1000 genomes]
rs10412139	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10412656	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10414373	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10420166	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10423403	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11085455	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1500400	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1500401	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1520071	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1520072	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1520073	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1607664	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1879235	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1963056	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1984771	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2056319	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2062564	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2090707	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2133816	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2133820	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2133821	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2173723	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2173724	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2246914	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2359162	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2454919	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2562399	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2562419	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2562441	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2562448	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2562451	0.88[EUR][1000 genomes]
rs2562452	0.88[EUR][1000 genomes]
rs2562453	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2562454	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2562455	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2562472	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2562473	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2650757	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2650759	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2650760	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2650787	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2650791	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2650794	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2650799	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2650806	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2650807	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2650827	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2650829	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2650830	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2650834	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2650835	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2681365	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2681366	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2681368	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2681371	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2681372	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2681375	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2681380	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2681382	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2681383	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2681384	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2681390	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34006898	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34978316	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35088652	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35366148	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58818104	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59654184	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62108277	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62108331	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62108332	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62108335	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6511261	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7254872	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7258901	0.89[EUR][1000 genomes]
rs74167858	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8100193	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8100318	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8102699	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8102854	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8106433	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8111788	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8113259	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
6	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers 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	31 gene(s)	inside rSNPs	diseases
7	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv510759	chr19:21664791-21723191	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2762028	chr19:21685778-21755476	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv963024	chr19:21686690-21722618	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1059328	chr19:21691123-21775948	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv543942	chr19:21711611-21767567	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2562465	ZNF429	cis	Whole Blood	GTEx
rs2562465	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs2562465	ZNF738	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21699600-21720800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
2	chr19:21699600-21727600	ZNF genes & repeats	Liver	Liver
3	chr19:21701000-21733400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:21701600-21720400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
5	chr19:21702400-21721400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:21702600-21717200	Weak transcription	Psoas Muscle	Psoas
7	chr19:21702800-21717200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:21702800-21718600	Weak transcription	Colon Smooth Muscle	Colon
9	chr19:21702800-21718600	Weak transcription	Fetal Heart	heart
10	chr19:21704000-21714600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
11	chr19:21704000-21717200	Weak transcription	NHDF-Ad	bronchial
12	chr19:21704400-21714400	Strong transcription	Primary T cells from cord blood	blood
13	chr19:21705000-21714200	Weak transcription	Fetal Thymus	thymus
14	chr19:21705000-21718600	Weak transcription	HSMM	muscle
15	chr19:21706400-21714000	Weak transcription	Osteobl	bone
16	chr19:21706400-21717200	Weak transcription	K562	blood
17	chr19:21707000-21714000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr19:21707000-21719000	Weak transcription	Stomach Mucosa	stomach
19	chr19:21708200-21716200	Strong transcription	Dnd41	blood
20	chr19:21708200-21717400	Strong transcription	Placenta	Placenta
21	chr19:21709000-21722800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:21709600-21716800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr19:21709600-21717200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:21710400-21714600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:21710600-21717200	Weak transcription	NH-A	brain
26	chr19:21711600-21715600	Strong transcription	Adipose Nuclei	Adipose
27	chr19:21711600-21716400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:21711600-21720400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
29	chr19:21711800-21714200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:21711800-21717400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:21712000-21715000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:21712000-21719200	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr19:21712200-21714400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
34	chr19:21712200-21714600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:21712200-21716800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:21712400-21714000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
37	chr19:21712400-21714400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr19:21712400-21714400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:21712400-21720400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
40	chr19:21712600-21714600	ZNF genes & repeats	Fetal Intestine Small	intestine
41	chr19:21712600-21715000	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr19:21712600-21716200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
43	chr19:21712600-21716600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr19:21712600-21720200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
45	chr19:21713000-21714200	Strong transcription	Stomach Smooth Muscle	stomach
46	chr19:21713000-21715200	Strong transcription	Fetal Lung	lung
47	chr19:21713200-21714200	ZNF genes & repeats	Spleen	Spleen
48	chr19:21713200-21714400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
49	chr19:21713200-21717200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr19:21713400-21714000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links