Variant report

Variant	rs234348
Chromosome Location	chr19:40467983-40467984
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	chr19:40467450..40469532-chr19:40475454..40478354,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000013275	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10421829	1.00[CHB][hapmap]
rs16973959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173062	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234329	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs234333	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs234335	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234336	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234337	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234338	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs234344	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234345	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234349	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234351	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234364	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234366	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234373	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531363	1.00[CHB][hapmap]
rs2542325	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2542328	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337796	1.00[CHB][hapmap]
rs376630	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378554	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399405	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs420413	1.00[CHB][hapmap]
rs512360	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58294889	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59616965	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60025633	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61413463	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249398	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7255173	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259136	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7260610	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8113194	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs913212	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40457400-40475600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr19:40460200-40474800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:40460800-40476000	Weak transcription	Psoas Muscle	Psoas
4	chr19:40461600-40475400	Weak transcription	Brain Substantia Nigra	brain
5	chr19:40464000-40475000	Weak transcription	GM12878-XiMat	blood
6	chr19:40465400-40474200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr19:40466200-40476200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:40466400-40469400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:40466400-40469400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr19:40466400-40469400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr19:40466400-40469400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr19:40466400-40469600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr19:40466400-40469600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr19:40466400-40474800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr19:40466400-40474800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:40467200-40469600	Weak transcription	Stomach Mucosa	stomach
17	chr19:40467400-40469600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:40467800-40468200	ZNF genes & repeats	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links