Variant report

Variant	rs378554
Chromosome Location	chr19:40465642-40465643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40463962..40466108-chr19:40471183..40473950,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs16973959	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173062	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234333	0.86[AFR][1000 genomes]
rs234335	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234336	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs234337	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234344	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234345	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs234347	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234348	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234349	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234351	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234362	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234363	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234364	1.00[ASN][1000 genomes]
rs234366	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234367	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234369	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234373	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542325	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2542328	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs376630	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512360	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58294889	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59616965	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60025633	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61413463	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249398	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7255173	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113194	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs913212	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[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	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40453000-40466000	Weak transcription	Fetal Intestine Small	intestine
2	chr19:40457400-40475600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr19:40458400-40466400	Enhancers	Primary B cells from peripheral blood	blood
4	chr19:40459600-40466200	Enhancers	Primary B cells from cord blood	blood
5	chr19:40460200-40474800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:40460800-40476000	Weak transcription	Psoas Muscle	Psoas
7	chr19:40461600-40475400	Weak transcription	Brain Substantia Nigra	brain
8	chr19:40462400-40466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:40463400-40466400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr19:40463600-40466400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr19:40463800-40466400	Enhancers	Primary T cells fromperipheralblood	blood
12	chr19:40463800-40467400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:40464000-40467200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr19:40464000-40467200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr19:40464000-40475000	Weak transcription	GM12878-XiMat	blood
16	chr19:40464800-40466200	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr19:40464800-40466200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:40464800-40466400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr19:40464800-40467000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:40465000-40465800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr19:40465000-40465800	Enhancers	Fetal Thymus	thymus
22	chr19:40465000-40466400	Enhancers	H9 Cell Line	embryonic stem cell
23	chr19:40465000-40466400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr19:40465000-40467200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr19:40465000-40467600	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr19:40465000-40467600	Enhancers	Placenta	Placenta
27	chr19:40465200-40465800	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr19:40465200-40466200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:40465200-40467000	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr19:40465200-40467200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr19:40465200-40467600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
32	chr19:40465400-40474200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr19:40465600-40466400	Enhancers	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links