Variant report

Variant	rs234337
Chromosome Location	chr19:40458725-40458726
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

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	0.91[AFR][1000 genomes];0.93[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	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs234335	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234336	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234338	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs234344	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234345	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234348	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234349	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234351	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234364	1.00[ASN][1000 genomes]
rs234366	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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];0.86[MKK][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]
rs2354775	1.00[JPT][hapmap]
rs2531363	1.00[CHB][hapmap]
rs2542311	1.00[JPT][hapmap]
rs2542325	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2542328	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337796	1.00[CHB][hapmap]
rs376630	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378554	0.89[AFR][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	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58294889	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59616965	0.92[AFR][1000 genomes];0.93[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];0.85[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	0.92[AFR][1000 genomes];0.93[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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs234337	EGR1	trans	brain	seeQTL
rs234337	EGR4	trans	brain	seeQTL
rs234337	PTGS2	trans	brain	seeQTL
rs234337	EGR2	trans	brain	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40450000-40461200	Enhancers	Primary T cells fromperipheralblood	blood
2	chr19:40450000-40461800	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr19:40451600-40458800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr19:40453000-40466000	Weak transcription	Fetal Intestine Small	intestine
5	chr19:40454400-40459200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:40454800-40459000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
7	chr19:40454800-40460000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:40455000-40460400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr19:40456000-40460400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:40456400-40459600	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr19:40457200-40459400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr19:40457200-40460200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:40457400-40475600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr19:40457600-40459200	Enhancers	GM12878-XiMat	blood
15	chr19:40457600-40459400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr19:40457600-40460000	Enhancers	Stomach Mucosa	stomach
17	chr19:40457600-40460200	Enhancers	Spleen	Spleen
18	chr19:40457800-40459600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr19:40458000-40459200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr19:40458000-40460400	Enhancers	Primary hematopoietic stem cells	blood
21	chr19:40458200-40459200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:40458200-40460200	Enhancers	Lung	lung
23	chr19:40458400-40458800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:40458400-40459200	Enhancers	Fetal Thymus	thymus
25	chr19:40458400-40459800	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr19:40458400-40460000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:40458400-40460000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:40458400-40460800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr19:40458400-40466400	Enhancers	Primary B cells from peripheral blood	blood
30	chr19:40458600-40458800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr19:40458600-40458800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
32	chr19:40458600-40459000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
33	chr19:40458600-40459000	Enhancers	Brain Hippocampus Middle	brain
34	chr19:40458600-40459200	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr19:40458600-40459200	Enhancers	Thymus	Thymus
36	chr19:40458600-40459600	Flanking Active TSS	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links