Variant report

Variant	rs6537552
Chromosome Location	chr10:50945088-50945089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10857535	0.86[JPT][hapmap]
rs1125165	0.80[AMR][1000 genomes]
rs12265707	0.86[EUR][1000 genomes]
rs1258168	0.83[CHD][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1258169	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1258170	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1258176	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1258178	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1258179	0.84[AMR][1000 genomes]
rs1258181	0.83[AMR][1000 genomes]
rs1258182	0.81[AMR][1000 genomes]
rs1258184	0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs1258245	0.80[EUR][1000 genomes]
rs1258246	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1258252	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1258253	0.81[EUR][1000 genomes]
rs1258256	0.83[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1258258	0.83[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1258260	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1268722	0.83[CHD][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1268723	0.84[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1270562	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1271629	0.84[GIH][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1659305	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17719642	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17775990	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1985896	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1992238	0.86[EUR][1000 genomes]
rs2083256	0.86[EUR][1000 genomes]
rs2377780	0.86[EUR][1000 genomes]
rs2889729	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4372365	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4838554	0.86[JPT][hapmap]
rs4838555	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs61846862	0.86[EUR][1000 genomes]
rs61846864	0.84[EUR][1000 genomes]
rs61846865	0.85[EUR][1000 genomes]
rs6537549	0.86[JPT][hapmap]
rs6537550	0.86[JPT][hapmap]
rs6537551	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816	0.83[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7069682	0.84[EUR][1000 genomes]
rs7088344	0.86[JPT][hapmap]
rs7100934	0.86[EUR][1000 genomes]
rs745836	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs745837	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs745838	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7916489	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv895378	chr10:50801342-50955649	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1048905	chr10:50928727-51019190	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50935200-50949600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:50940400-50949600	Weak transcription	Fetal Heart	heart
3	chr10:50940400-50953400	Weak transcription	Brain Hippocampus Middle	brain
4	chr10:50940600-50966000	Strong transcription	Liver	Liver
5	chr10:50941000-50946400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr10:50941000-50951600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr10:50941200-50965400	Weak transcription	Brain Germinal Matrix	brain
8	chr10:50942000-50946400	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr10:50942000-50949600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr10:50942800-50946200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr10:50942800-50946400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr10:50943000-50946600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr10:50943000-50956400	Strong transcription	Brain Anterior Caudate	brain
14	chr10:50943200-50945400	Strong transcription	Ovary	ovary
15	chr10:50943200-50946800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr10:50943200-50969400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr10:50943400-50946600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
18	chr10:50943400-50949400	Weak transcription	Fetal Intestine Large	intestine
19	chr10:50943400-50956200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:50943600-50946200	Strong transcription	Fetal Brain Female	brain
21	chr10:50943600-50947200	Strong transcription	Brain Cingulate Gyrus	brain
22	chr10:50943600-50949600	Strong transcription	Fetal Intestine Small	intestine
23	chr10:50943800-50948000	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr10:50943800-50956000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr10:50944000-50945200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr10:50944000-50946400	Strong transcription	Brain Angular Gyrus	brain
27	chr10:50944000-50969400	Weak transcription	Brain Substantia Nigra	brain
28	chr10:50944200-50945600	Strong transcription	Pancreas	Pancrea
29	chr10:50944200-50946000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr10:50944400-50946400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr10:50944400-50950000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr10:50944400-50952400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr10:50944800-50951600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr10:50945000-50945200	Enhancers	Spleen	Spleen

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