Variant report

Variant	rs2401987
Chromosome Location	chr5:16682770-16682771
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10060275	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10060411	0.98[ASN][1000 genomes]
rs11738070	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11740825	0.82[CEU][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11741866	0.81[AMR][1000 genomes]
rs1560087	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1560088	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1863996	0.84[MEX][hapmap];0.83[YRI][hapmap]
rs2288432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2288433	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2288434	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2288435	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288436	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2288437	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2303703	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256929	0.84[MEX][hapmap]
rs256935	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs257050	0.82[CEU][hapmap]
rs26745	0.93[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs26746	0.94[ASN][1000 genomes]
rs26748	0.95[ASN][1000 genomes]
rs26749	0.95[ASN][1000 genomes]
rs26750	0.97[ASN][1000 genomes]
rs26757	0.97[ASN][1000 genomes]
rs26758	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.99[ASN][1000 genomes]
rs27350	0.93[ASN][1000 genomes]
rs27501	1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs27553	0.93[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs27880	0.93[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28056	0.93[ASN][1000 genomes]
rs28057	0.93[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs399833	0.93[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.99[ASN][1000 genomes]
rs4701670	0.82[CEU][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs4702166	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58619409	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59574363	0.81[AMR][1000 genomes]
rs6860226	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6881621	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6889243	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717840	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7733988	0.84[MEX][hapmap]
rs7735007	0.97[ASN][1000 genomes]
rs890911	0.85[ASW][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][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
rs2401987	GSTT1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16661600-16689400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:16661800-16700000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:16663000-16712400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:16663600-16695400	Strong transcription	Fetal Intestine Small	intestine
5	chr5:16663800-16690800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:16663800-16694400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:16663800-16698000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:16663800-16702400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:16663800-16713400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:16664000-16701000	Strong transcription	Fetal Intestine Large	intestine
11	chr5:16664000-16702000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:16664000-16702200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:16664000-16702400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:16664200-16702200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:16664600-16690600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr5:16665600-16699200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:16667400-16683600	Weak transcription	Liver	Liver
18	chr5:16667800-16701000	Weak transcription	Right Ventricle	heart
19	chr5:16670800-16686000	Strong transcription	Fetal Stomach	stomach
20	chr5:16671000-16691000	Strong transcription	Fetal Muscle Trunk	muscle
21	chr5:16671200-16690200	Strong transcription	HUVEC	blood vessel
22	chr5:16671800-16685400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:16673800-16713400	Weak transcription	Psoas Muscle	Psoas
24	chr5:16674200-16687000	Strong transcription	Fetal Lung	lung
25	chr5:16674200-16693000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:16675000-16690400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr5:16675400-16683000	Weak transcription	Aorta	Aorta
28	chr5:16675800-16713600	Weak transcription	Left Ventricle	heart
29	chr5:16676200-16684600	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr5:16677600-16690200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:16677800-16690800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:16677800-16706000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:16678000-16684600	Strong transcription	Brain Angular Gyrus	brain
34	chr5:16678000-16685800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:16678000-16686200	Strong transcription	Fetal Brain Female	brain
36	chr5:16678000-16691000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:16678000-16691400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr5:16678200-16684200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:16678200-16684200	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr5:16678200-16684200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:16678200-16686000	Strong transcription	NHEK	skin
42	chr5:16678200-16687600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:16678200-16690200	Strong transcription	HepG2	liver
44	chr5:16678200-16690800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr5:16678200-16691000	Strong transcription	Fetal Muscle Leg	muscle
46	chr5:16678200-16691000	Strong transcription	NH-A	brain
47	chr5:16678200-16691200	Strong transcription	A549	lung
48	chr5:16678400-16684200	Strong transcription	Brain Germinal Matrix	brain
49	chr5:16678400-16684600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr5:16678400-16686000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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