Variant report

Variant	rs1863996
Chromosome Location	chr5:16689794-16689795
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11738070	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11740825	0.86[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11741866	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1560087	0.86[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1560088	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2303703	0.83[MEX][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs2303704	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2401987	0.84[MEX][hapmap];0.83[YRI][hapmap]
rs256930	0.84[MEX][hapmap]
rs256935	0.84[EUR][1000 genomes]
rs257047	0.81[EUR][1000 genomes]
rs257049	0.86[EUR][1000 genomes]
rs257050	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs257051	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs257198	0.86[EUR][1000 genomes]
rs4701670	0.86[CEU][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4702166	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58619409	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59574363	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6860226	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6881621	0.86[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6889243	0.80[AFR][1000 genomes]
rs7717840	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7733988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs890911	0.84[ASW][hapmap];0.82[CEU][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869660	chr5:16651289-16766428	Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv4737	chr5:16681166-16707357	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1863996	GSTT1	trans	lymphoblastoid	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16661800-16700000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:16663000-16712400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:16663600-16695400	Strong transcription	Fetal Intestine Small	intestine
4	chr5:16663800-16690800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr5:16663800-16694400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:16663800-16698000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:16663800-16702400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:16663800-16713400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:16664000-16701000	Strong transcription	Fetal Intestine Large	intestine
10	chr5:16664000-16702000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:16664000-16702200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:16664000-16702400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:16664200-16702200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:16664600-16690600	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr5:16665600-16699200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:16667800-16701000	Weak transcription	Right Ventricle	heart
17	chr5:16671000-16691000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr5:16671200-16690200	Strong transcription	HUVEC	blood vessel
19	chr5:16673800-16713400	Weak transcription	Psoas Muscle	Psoas
20	chr5:16674200-16693000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:16675000-16690400	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:16675800-16713600	Weak transcription	Left Ventricle	heart
23	chr5:16677600-16690200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:16677800-16690800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:16677800-16706000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:16678000-16691000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:16678000-16691400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr5:16678200-16690200	Strong transcription	HepG2	liver
29	chr5:16678200-16690800	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr5:16678200-16691000	Strong transcription	Fetal Muscle Leg	muscle
31	chr5:16678200-16691000	Strong transcription	NH-A	brain
32	chr5:16678200-16691200	Strong transcription	A549	lung
33	chr5:16678400-16690000	Strong transcription	Brain Anterior Caudate	brain
34	chr5:16678400-16690000	Strong transcription	Brain Hippocampus Middle	brain
35	chr5:16678400-16690200	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr5:16678400-16690600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:16678400-16691000	Strong transcription	Lung	lung
38	chr5:16678600-16691000	Strong transcription	HMEC	breast
39	chr5:16678600-16695000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:16678800-16690200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
41	chr5:16678800-16690200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr5:16679600-16693200	Weak transcription	Esophagus	oesophagus
43	chr5:16679600-16701000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr5:16680200-16695000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:16680400-16690600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr5:16681000-16693400	Weak transcription	Fetal Brain Male	brain
47	chr5:16681000-16699200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr5:16681400-16701000	Weak transcription	Colonic Mucosa	Colon
49	chr5:16681600-16713200	Weak transcription	Small Intestine	intestine
50	chr5:16682400-16699200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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