Variant report

Variant	rs2965242
Chromosome Location	chr19:53756193-53756194
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53756061..53758221-chr19:53835400..53837964,2	K562	blood:

Variant related genes	Relation type
ENSG00000213799	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10401578	0.88[CHB][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs10404048	0.80[CHB][hapmap]
rs10425196	0.84[ASN][1000 genomes]
rs10775558	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs10853858	0.81[CHD][hapmap]
rs10853859	0.82[CHB][hapmap]
rs11084227	0.88[CHB][hapmap];0.83[CHD][hapmap];0.84[ASN][1000 genomes]
rs11084228	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1129002	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666631	0.90[ASN][1000 genomes]
rs12972588	0.88[ASN][1000 genomes]
rs12982260	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12984188	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12984473	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12985503	0.86[ASN][1000 genomes]
rs17272966	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28411117	0.97[ASN][1000 genomes]
rs2865241	0.93[ASN][1000 genomes]
rs28734122	0.83[ASN][1000 genomes]
rs2914371	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2914372	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2914376	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2914377	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2914378	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2914381	0.80[CHB][hapmap]
rs2914383	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2914384	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2965222	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2965224	0.80[CHB][hapmap]
rs2965231	0.80[CHB][hapmap]
rs2965236	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2965237	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2965238	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2965240	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2965243	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2965244	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3097248	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3111319	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36114232	0.84[ASN][1000 genomes]
rs4801965	0.81[CHB][hapmap]
rs4801970	0.82[CHB][hapmap]
rs4803069	0.83[ASN][1000 genomes]
rs4803071	0.96[ASN][1000 genomes]
rs4803080	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55779655	0.96[ASN][1000 genomes]
rs62117791	0.95[ASN][1000 genomes]
rs7247982	0.80[CHB][hapmap]
rs8113436	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9788	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers 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	39 gene(s)	inside rSNPs	diseases
4	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
7	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	esv2830362	chr19:53681132-53933147	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1055236	chr19:53739483-53778339	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1059899	chr19:53744560-53768337	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS 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	3 gene(s)	inside rSNPs	diseases
12	nsv1064070	chr19:53744560-53769702	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS 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	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2965242	ZNF418	cis	cerebellum	SCAN
rs2965242	ZNF304	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53735800-53756200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:53737400-53757600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:53738800-53756600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
4	chr19:53739600-53756200	ZNF genes & repeats	Fetal Brain Female	brain
5	chr19:53740000-53756400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:53740000-53756600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
7	chr19:53740000-53756800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:53740200-53756800	ZNF genes & repeats	Fetal Lung	lung
9	chr19:53740200-53757600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:53740400-53756800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
11	chr19:53743000-53756600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr19:53745200-53756600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:53747800-53757000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr19:53748400-53757400	Weak transcription	Colonic Mucosa	Colon
15	chr19:53749600-53756200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
16	chr19:53749800-53756600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:53750000-53757200	Weak transcription	HUVEC	blood vessel
18	chr19:53750200-53756600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:53750400-53759200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
20	chr19:53750600-53756200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
21	chr19:53750600-53757600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:53751200-53757400	ZNF genes & repeats	Primary B cells from cord blood	blood
23	chr19:53751600-53756800	ZNF genes & repeats	Ovary	ovary
24	chr19:53751800-53756800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
25	chr19:53752000-53757000	ZNF genes & repeats	Fetal Intestine Large	intestine
26	chr19:53752000-53757200	Weak transcription	NH-A	brain
27	chr19:53752200-53756600	Weak transcription	Fetal Thymus	thymus
28	chr19:53752200-53756600	Strong transcription	Osteobl	bone
29	chr19:53752400-53756200	ZNF genes & repeats	Aorta	Aorta
30	chr19:53752400-53756800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:53752400-53759400	ZNF genes & repeats	Liver	Liver
32	chr19:53752600-53756400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:53752600-53757400	Weak transcription	Stomach Mucosa	stomach
34	chr19:53752800-53756200	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr19:53752800-53756200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr19:53752800-53756600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:53752800-53756600	Strong transcription	Placenta	Placenta
38	chr19:53753000-53756200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr19:53753000-53756400	Strong transcription	Brain Substantia Nigra	brain
40	chr19:53753200-53756200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
41	chr19:53753400-53756200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:53753400-53756200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:53753400-53756600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:53753400-53756600	ZNF genes & repeats	Primary T cells from cord blood	blood
45	chr19:53753600-53756200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr19:53753600-53756200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:53753600-53756600	Strong transcription	Rectal Smooth Muscle	rectum
48	chr19:53753600-53756800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
49	chr19:53753600-53757400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
50	chr19:53753600-53759000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood

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