Variant report

Variant	rs542394
Chromosome Location	chr3:43027875-43027876
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10470680	0.84[EUR][1000 genomes]
rs11129987	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11129988	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1346414	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1346415	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17074894	0.82[EUR][1000 genomes]
rs1816227	0.80[EUR][1000 genomes]
rs2288371	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2288372	1.00[JPT][hapmap]
rs2288373	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs28378297	0.81[EUR][1000 genomes]
rs3915020	0.83[EUR][1000 genomes]
rs526511	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs545023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs551658	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57113579	0.82[ASN][1000 genomes]
rs57664746	0.82[ASN][1000 genomes]
rs57795561	0.82[ASN][1000 genomes]
rs59789275	0.95[ASN][1000 genomes]
rs60046829	0.95[ASN][1000 genomes]
rs60549782	0.82[ASN][1000 genomes]
rs60607395	0.95[ASN][1000 genomes]
rs60616619	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61004728	0.84[EUR][1000 genomes]
rs61102947	0.95[ASN][1000 genomes]
rs615462	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs619660	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62248962	0.80[EUR][1000 genomes]
rs62249006	0.84[EUR][1000 genomes]
rs62249007	0.84[EUR][1000 genomes]
rs62249008	0.82[EUR][1000 genomes]
rs62249009	0.84[EUR][1000 genomes]
rs62249011	0.84[EUR][1000 genomes]
rs62249013	0.82[EUR][1000 genomes]
rs638602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649682	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6763762	0.84[EUR][1000 genomes]
rs6773223	0.83[EUR][1000 genomes]
rs6775999	0.84[EUR][1000 genomes]
rs6778645	0.87[ASN][1000 genomes]
rs6798412	0.84[EUR][1000 genomes]
rs6798520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704895	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs704899	1.00[CEU][hapmap]
rs72869044	0.82[ASN][1000 genomes]
rs72869047	0.82[ASN][1000 genomes]
rs7617715	0.81[EUR][1000 genomes]
rs7621158	0.95[ASN][1000 genomes]
rs7625959	1.00[JPT][hapmap]
rs7641452	0.80[EUR][1000 genomes]
rs7644923	0.83[EUR][1000 genomes]
rs834183	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs834325	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs834579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs834584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs834699	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311330	0.81[EUR][1000 genomes]
rs9311331	0.84[EUR][1000 genomes]
rs9808932	0.82[EUR][1000 genomes]
rs9832875	0.80[EUR][1000 genomes]
rs9833284	0.84[EUR][1000 genomes]
rs9852930	0.82[EUR][1000 genomes]
rs9858270	0.82[EUR][1000 genomes]
rs9874514	1.00[CHB][hapmap];0.85[JPT][hapmap]

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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv460523	chr3:43025986-43063406	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv590150	chr3:43025986-43063406	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43021400-43030200	Weak transcription	Aorta	Aorta
2	chr3:43022000-43033000	Weak transcription	Pancreas	Pancrea
3	chr3:43022000-43037000	Weak transcription	Right Atrium	heart
4	chr3:43022200-43032800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:43022800-43030000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:43023000-43037800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:43023200-43029600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:43023400-43029600	Weak transcription	Liver	Liver
9	chr3:43026000-43029600	Weak transcription	Ovary	ovary
10	chr3:43026000-43030000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:43026600-43028200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:43026600-43030400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:43026600-43032000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:43026600-43032400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:43026600-43032800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:43026800-43029800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:43026800-43030200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:43026800-43032400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:43027000-43029800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:43027000-43029800	Weak transcription	Brain Substantia Nigra	brain
21	chr3:43027000-43033200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:43027200-43029600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:43027200-43029600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:43027200-43032800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:43027400-43029600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:43027400-43029800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:43027400-43032200	Weak transcription	Fetal Thymus	thymus
28	chr3:43027600-43028200	ZNF genes & repeats	Fetal Intestine Small	intestine
29	chr3:43027800-43028200	Enhancers	Thymus	Thymus

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